There were a few conditions that led to document check-in errors in 6R2. For example where the document wasn't fully delivered into the TRIM store before the user exited an application or TRIM or both. Also some auto generated PDF's (say from a bulk scanner) into a TRIMQ had failures.
These errors were believed to be fixed in 7.1x. I'm thinking since your rate of error is 1 in 10,000 that it might be a user issue. E.g. end of day close all documents, close TRIM, close email, log-off and go home. In this scenario it is feasable that changed documents may not have had enough time to save and upload.
I did a whol;e lot of testing trying to replicate the issue - registering a large doc from usb stick and yanking it out, hitting power button and the like. TRIM performed flawlessly - either completeing or rolling back.
Starting to disbelieve users as finding some zero byte records sitting in Offl;ine Records just waiting to be put into TRIM with the inevtable consequences.
However, it would be nice if TRIM would perform a check at registration seeing It gives an error when they are viewed. Hmm, I'll put up an enhancenment request shortly.