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Buy now & saveWelcome to the Community space, @MrLizard06. Let's team up and get you through this to fix the markup option inside QuickBooks Desktop (QBDT).
Before anything else, we commend you for giving us a glimpse of your current situation inside the program. In this case, you'll want to review the inventory settings and see if everything is set according to your preference. We'll gladly write down the steps to get you going:
If the issue persists after making changes or reviewing the setup, we recommend utilizing the Verify and Rebuild feature. This way, the program will conduct a system checkup to determine the cause of the problem and start fixing it. For more information, please see this page: Verify and Rebuild Data in QuickBooks Desktop.
In addition, you can run a report to help you keep track of your inventories and transactions inside QBDT: Understand reports.
You can comment below if you need assistance managing inventory markup or estimates inside the program. As always, we'll be around to respond as soon as possible and help you with your concerns. Keep safe.