Since it's not a QuickFilter, perhaps also make sure you're not in a Smart Folder or that the sorting options aren't making it hard to locate the Entries—even newly created Entries may be getting submitted, but ending up in an unexpected spot in the overall list. To sort by Date, click the Date column header.
If that doesn't do it, it could be an anomaly that's unique to the data in that one Account. We definitely want to look into this further, but that would require that we setup the same situation here using your same data so that we can replicate the issue and watch what happens behind-the-scenes as it occurs. Any chance you'd be willing to send a backup data file to us via email?
If so, choose 'Backup Accounts...' from the File menu, save the backup to someplace accessible, and attach it to an email to
support@splasm.com.
Also, seeing a System Information report created just after the issue occurs wherein new Entries can't be added would be helpful. For that, try to add a new Entry, exit CheckBook Pro, launch System Information.app from inside the Applications > Utilities folder, and then use the Save option under the File menu. Then, attach the resulting file to an email.
Thanks!