I don't think this has anything to do with settings, but possibly a flaw in the software.
I use the work-in-progress folder extensively and on several ocassions in GW 5.5 and also in 6.0, my messages have disappeared while in the process of editing them. Case in point: I was in the process of working on a large message one day and during the course of creating and editing it, I opened and closed it several times, maybe 6-8. When I finalized the message and saved it to the file, instead of asking me to save this to the folder, it just disappeared, but not to trash. I did a search, but it was gone. Still other times, the message appears to be saving to this folder, but when I open it, it's not.
Because several of my users have complained of the same issue, I can only conclude that the problem is this folder.
Regards,
Stars