I see you previously had a ticket open with my colleague Evan about a similar problem last year - has this issue been ongoing since then, or has it just started cropping up again recently?
Ideally, to properly troubleshoot this we'd need a copy of the latest revision of your repository and a backup or SQL Compare snapshot of your database - if you feel comfortable providing that, could you email it to firstname.lastname@example.org
and quote ticket number #22352? If you need, we can set up an FTP area for large files. Thanks for your help with this!