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This guide is provided by Conductor, the service that powers the QuickBooks Desktop integration for many business tools, including the one that sent you here.
Any pop-up in QuickBooks Desktop, or a Windows prompt in front of it, stops the Web Connector from reaching your company file. Nothing syncs until a person answers it on the computer that runs the Web Connector. Conductor cannot click it for you. Not at that computer? Send this page to whoever can sign in to it. A warning this ordinary is enough. Open windows such as an invoice do not block, though closing them is a cheap extra step.

How you know

  • Your app says “QuickBooks is waiting for input on a pop-up or modal window” (0x80040414).
  • Requests keep failing with “Request timed out after 90 seconds, before it was sent to QuickBooks Desktop” (60 in some apps), then “Your QuickBooks Desktop connection is not active right now”.
  • The “Last QBD heartbeat” in the Conductor dashboard may stop moving.
  • The Web Connector shows “Error connecting to QuickBooks - close any modal dialog in QuickBooks.” in red, or QBWC1053 in its log.
The Windows prompt to “allow this app to make changes to your device” gives the “configuration issue” error (0x80040408) instead. A lone timeout often has another cause.

Fix it now

1

Look now, on the Web Connector's computer

Sign in as the Windows user that runs the Web Connector while the errors are still coming. The pop-up shows only there, never in another login or computer, and stays until someone answers it. Bring QuickBooks to the front; look behind it and on the taskbar. On Rightworks with several logins, check each one.
Connecting by Remote Desktop from a screen of a different size can itself raise the theme warning below. To leave, close the Remote Desktop window; signing out of that Windows user closes QuickBooks and the Web Connector.
2

Screenshot the pop-up, then answer it

Capture the whole screen first; the lasting fix depends on which pop-up it is. Then answer it as Which pop-up is it? describes (for a plain warning, click OK) and retry.
One prompt must be answered, not closed: QuickBooks asking whether an application may access the company file. As the QuickBooks Admin, choose the Yes, always option.
3

Still stuck? Restart QuickBooks and the Web Connector

  1. In the Web Connector, click Exit.
  2. Close QuickBooks Desktop if it responds.
  3. Open Task Manager (Ctrl + Shift + Esc), click More details if shown, open the Details tab, and end any QBW.exe or QBW32.exe still running in your Windows user.
  4. Open QuickBooks Desktop, answer any prompt (see the Note above), and leave it open.
  5. Click Start, type Web Connector, open it, and click Hide.
Found no pop-up? Follow the connection not active or cannot connect guide.

Which pop-up is it?

”Use your Intuit Account to sign in to QuickBooks”

QuickBooks asks the company file’s owner (the Primary Admin) to sign in to an Intuit account; another version starts “You have been signed out”. Cancelling only postpones it, and no setting turns it off. Have the Primary Admin sign in on the Web Connector’s computer, in its Windows user, in every company file it syncs, and again every 180 days.

”Do you want to allow this app to make changes to your device?”

When it names “QuickBooks Utility Application”, the Web Connector had to start QuickBooks itself, because QuickBooks was closed or open under another Windows user or permission level. Clicking Yes has not restored syncing in any case we have seen. Keep QuickBooks open in the Web Connector’s Windows user and have it open at startup. If it still appears while QuickBooks is open, follow our guide to this prompt.

”Bank Feeds In Use”, “The company file cannot be closed”, or “An Integrated Application is currently sharing data”

For “Bank Feeds In Use”, the person it names must click Release Exclusive Use in the Bank Feeds menu (in your own QuickBooks, if the name is yours), then someone clicks OK on the Web Connector’s computer. We know of no setting that prevents it, so ask whoever uses Bank Feeds to release it when they finish. “The company file cannot be closed” also waits for OK on the Web Connector’s computer. “An Integrated Application is currently sharing data” only stops a person who closes QuickBooks or signs out while a sync runs. Running the Web Connector where nobody works keeps it away.

”The system Theme settings have changed”

QuickBooks shows this when the display of its Windows session changes, most often after a Remote Desktop connection from a screen of a different size. In your own Windows user, it only interrupts you. In the Web Connector’s Windows user, it blocks syncing until someone clicks OK, and no setting turns it off. Then stay out of that Windows user; watch your app’s errors. When you must connect, use the same computer and window size. That lowers the odds; it has appeared with nobody connected.

Reminders and backup reminders

QuickBooks reminders block syncing when they pop up. If nobody does daily work in the Web Connector’s QuickBooks, turn them off there under Edit → Preferences → Reminders, and clear Remind me to back up when I close my company file in the backup options.

Update prompts

Update prompts block syncing, and an update cancelled halfway can leave QuickBooks unusable until it finishes. Install updates on purpose, at a set time, in the Web Connector’s Windows user. Then check that no prompt remains and that only one QuickBooks version is installed.

Ads and messages about Intuit products and services

Signed in as the QuickBooks user the connection uses, go to Edit → Preferences → General → My Preferences and check Turn off pop-up messages for products and services; it applies to that user only. Check Do not display this message in the future when offered. Neither stops the sign-in prompt, payroll messages, or the theme warning, and new ads keep coming.

”QuickBooks - Unrecoverable Error”, “QuickBooks has stopped working”, or “FATAL ERROR”

For “QuickBooks - Unrecoverable Error” and “QuickBooks has stopped working”, click Close program or Don’t Send. For “FATAL ERROR”, click OK. Each means QuickBooks crashed. Reopen it and leave it open. Crashes we have seen often followed the Web Connector starting QuickBooks many times a day, so have it open at startup. Install QuickBooks updates, and if crashes continue, check the company file for damage.

”QBWC1085”, “Unhandled exception has occurred”, or “Quickbooks Web Connector has stopped working”

For QBWC1085, delete the Web Connector log file. For “Unhandled exception has occurred”, click Continue, then delete the log file. For “Quickbooks Web Connector has stopped working”, make sure only one QuickBooks version is installed; a damaged log file can cause it too. If a box draws no buttons, as can happen over Remote Desktop, press Enter for its default button.

”Error 1328”, “Internet Security Levels Are Set Too High”, or a payroll warning

For “Error 1328”, do not click “Ignore”, which only leads to more errors; remove extra QuickBooks versions instead. “Internet Security Levels Are Set Too High” blocks syncing until someone answers it. Any warning with only an OK button, like this payroll warning, blocks syncing until someone clicks it.

Prevent it

A Windows user that stays signed in and that nobody works in avoids many pop-ups. Keep QuickBooks open there, at No Company Open if the computer syncs several company files, disconnect from Remote Desktop instead of signing out, have the Primary Admin sign in to the Intuit account in each company file every 180 days, turn off reminders, and keep one QuickBooks version installed. The ideal QuickBooks Desktop setup covers each step. Nobody watches that screen, so a pop-up there can sit for hours: watch your app’s errors. If you build on Conductor, send a Health Check request before scheduled jobs; it fails while a pop-up blocks. If you manage that computer, skip tools that click pop-ups away: they cannot tell an ad from a payroll warning, press the default button, need an unlocked session, and hide the cause.

Pop-ups you can ignore

These look like errors but are harmless:
  • “QBWC1031: Update completed with some error” means there were no new requests. To hide it, click File → Disable Notifications in the Web Connector.
  • “Update postponed by application” means nothing needed to sync.
  • “An error occured while loading a another instance of QuickBooks Web Connector” means the Web Connector was opened twice. Click OK.
QBWC1058 at every Windows sign-in, offering to replace, duplicate, or skip the connection, must be answered before the Web Connector runs: click Cancel, then remove whatever opens the connection’s .qwc file at sign-in, such as a shortcut in the Startup folder. If pop-ups keep stopping your syncs, email support@conductor.is with a screenshot of the whole screen in the Web Connector’s Windows user, taken while the error is happening.