I'm almost 100% sure that simulation does not affect a download into the remote as the binary files are generated and stored in completely separate folders. I don't understand why things are going awry but there's got to be something different that you are doing in the process of downloading to get a working config. With regard to a corrupt PCF. If it were corrupt, it would likely not load/download.

However, if you are so inclined, email me a copy and I'll run a few checks on it just to be sure.