Some antivirus program was one thing I was thinking as well.....
In our scenario we do have Flexi split up. We have a dedicated RIP system which (Windows 7 x64) its ONLY purpose is to run Production Manager. We do not use that machine for anything else, especially surfing the web or anything so it has no antivirus software or any other software loaded except for the drivers needed for the specific machines connected to it and Production Manager. From our desktops we run the main Flexi Design program (it connects over the network to the Production Manager to send jobs) as well as other programs. Those do have Microsoft Security Essentials and on each we have specifically excluded the Flexi folders (including the Flexi temp files folders) from any sort of virus scanning. Our primary Client Files (network share from our SAN that we all connect to) is also excluded from virus scanning. We do have multiple levels of protection though - any files introduced to our systems or network are scanned either as the removable drive, disc, or files are downloaded, saved from emails, etc. Our security gateway (Checkpoint) has antivirus, antimalware, spam blocking, and more which catches things incoming from the internet at the edge plus MSE on each desktop.
One thing I would at minimum do though is whatever antivirus software you have should have a setting to exclude certain folders or file types. I'd make sure it is configured to exclude scanning the Flexi folders (including the Flexi temp files folder) and maybe even by file type make sure it excludes .fs files. Some antivirus software when scanning a file can put a momentary lock on the file which can cause all sorts of issues with some other programs that might be using the file. Especially if the antivirus software momentarily locks a file that it detects in use and decides to do a quick scan on.
Another thing to look at is your Windows Event Viewer. In there you should be able to find errors from when Flexi crashed and might be able to find some clues about what caused the crash. Sometimes an error will indicate some particular driver file was being accessed like a video card driver or something.... Its quite possible that you might just need to update a video card driver, network card driver, or some other driver on your machine. Quite often a device manufacturer might have a driver for something that for 99% of things works just fine but has some obscure bug that freaks out just one program. Of course the victim points their finger at the program for misbehaving when in reality it is some poorly coded driver...