Our Tool Room uses Surfcam to generate CAM files. I mention it because I'm not sure if this issue is isolated to Surfcam or not but they are the first to really track this down.
The users have the CAM file in a Build/WIP state and it is Checked Out. They work on the file, then save. From within Surfcam everything seems normal but if we monitor the PDM folder the file is unmodified, the date code is not updated, and a new file with the same name but different extension is created. It's like PDM rejects or interrupts the save process somehow.
If they save the CAM file outside the vault, then drag it into the vault everything updates correctly.
This is a big problem right now because they can't trust that new versions are being saved properly and we may end up having them drag files in/out of the vault to ensure the new files are accepted