Phil -
Are you sure everything is actually synching up correctly in general?
1. If you go to QuickBooks > Synchronize, what do you have there as the last Full Synchronization date?
2. What about the last Changes-Only Synchronization date?
3. If you open up the brown "M" on your desktop next to the clock (this is the Method Integration Engine), does the Activity Log show any kind of error messages if you clear it out (just right click, Select All, right click Cut), and then do a sync (Synchronization > Changes-Only Synchronization). I know it's kind of hard to read, but it should be fairly obvious if something isn't jiving.
4. Have you switched files lately? For example, did you have this account attached to one QuickBooks file and then later attached it to another QuickBooks file?
Sorry for so many questions. But something seems off. Based on your problems with the BillPaymentCheck (which really should be working for you).......it looks like your synch is off in general on this account.
Paul