Does anyone have issues with quickbooks payroll not recognizing vacation and paid time off when you run payroll salaried employees and deducting it from their balances?

I appreciate you for sharing the details of your concern, jclark4. Let me route you to the best help available so this gets sorted out immediately.

The payroll items and your salaried employees' time off will normally sync to QuickBooks Online Payroll if the integration process is set up correctly. That said, you'll want to ensure your QuickBooks Time is set up with your QuickBooks Online Payroll account.

If you have ensured the setup is correct, I recommend contacting our Technical Support Team. One of our experts has the necessary tools to check your account securely and perform a screen-sharing session to investigate this behavior further.

1. Log in to your QuickBooks Online account.
2. Click the ? Help button at the top right corner.
3. Go to the Search tab, then select Contact Us.
4. Enter a brief discussion about your concern, then click Continue.
5. Choose a way to connect with us.

Here's an article that contains the time when the support is available, depending on your type of subscription. Just go to this article's QuickBooks Online Payroll section for more info: Contact Payroll Support.

Additionally, you can pull up a variety of payroll reports in QuickBooks. This will give you a closer look at your employee's total wages, deductions, and tax information in a certain period. For the complete list of available payroll reports and how to pull them up, kindly refer to this article: Run payroll reports.

Feel free to comment below if you have any other questions about QuickBooks Online. I'll always be around to lend a hand. Stay safe!

Yes, I have already done this. I was on a 6-hour call with 5 different people that blamed the other person's department and in the end was told I have to manually enter the time in because they didn't know how to fix it. 

Thanks for getting back with the Community, jclark4.
 

Since QuickBooks isn't recognizing a pay type you've set up when you try to process payroll, I'd recommend confirming the time off policy is configured properly.
 

Here's how:
 

1. In your left navigation bar, go to Payroll, then Employees.
2. Click the employee's display name.
3. From your Pay types section, hit Start or Edit.
4. Find the Time off policies area.
5. Locate your policy and press its Edit () option.
6. Review the setup. If any changes need to be made, make them.
7. When you're finished, select Save, then Save.

You'll also want to confirm your time off is set up correctly in QuickBooks Time.
 

I've also included a detailed resource about working with time off policies which may come in handy moving forward: Set up & track time off in payroll
 

Please feel welcome to send a reply if there's any questions. Have a lovely day!