In the latest version, 2.5.3, deleted Categories shouldn't reappear for Autocompletion suggestions. Definitely get updated to the latest by choosing 'Check for Updates...' from the CheckBook menu. If that doesn't do the trick, there could be an overall saving issue due to damage in your Accounts file so we'll want to gather additional information. Would you be willing help us by sending the following to
support@splasm.com?
1. A System Information report. This report tells us how your Mac is configured. You can create one of these reports by clicking the Finder icon in your Dock, going to the Go menu at the top of your screen, clicking the Utilities menu item, opening System Information.app, then going to the File menu and clicking the Save... menu item.
2. Your recent system.log files. These files contain routine status messages from apps, but they also contain any error messages these apps may have logged, in addition to any error messages the Mac itself may have logged. We need to see these to get an accurate picture of when the app started to misbehave and to possibly explain why. You can find these by clicking the Finder icon in your Dock, going to the Go menu at the top of your screen, clicking the Go to Folder... menu item, then going to the /var/log folder. Send every file whose name begins with the word "system".
Concerning the change in update downloads, unfortunately, adhering to Apple's latest security measures has made it impossible for us to use the prior manner of downloading within the application. We're still looking into making that possible again, though.