Okay, this will be an extended cauldron run. I'm running in the same order as I did before. But I will install each module into v0.54, dated Feb 4, then compress the result. I will then uncompress and see if I get any choose the file silliness. If I don't, I will go on to the next module and repeat the process until I get the file replacement dialog. That will isolate the problem.
Stand by for carnage!