It sounds like an issue with writing to the SQL Archiver database. This will make the system save the video files to the HDD, but not have any index of where the video is located.
To fix the issues going back, there is an Orphan Video file finder, which is in the Genetec Program Files foldler. This utility can scan your recording HDD, compare the files with what records exist in the SQL database, and it can re-index the SQL database so that the past recordings are found and will be back in the normal video retention time rules. Otherwise if the database doesnt know the files exist, they wont be automatically scrubbed after your automatic delete dates (15, 30, 60 days).
Edit: Also as a side note, you can always post to the Genetec Forums at gtap.genetec.com and get quicker, more open answers from Genetec certified staff, other end users, etc. Full Fake Disclosure: I am the unofficial official Genetec Forum Fanboy.