I can't say I've encountered this but someone else may have. However it would help if you could give more details of exactly what you are doing.
So do you have two instances of the DBP editor open, each with their own source code, which you alternately compile? Or have you already compiled both and are alternately running them? What exactly is it that you are opening and deleting? The dba and dbpro files, the exe files or both?
My initial hunch based on not very much would be that this is something to do with having a dba source file linked to a couple of dbpro files but that really is just a guess until you give us more info.
Hopefully I or someone else will be able to help more once you give us a few more details.
Oh and why do you call it a "memory glitch"? Is there any error message that says that?