JTCS and the Windows 7 file system?

[Crossroads]

Question for the techies out there, hopefully you can help me out?

I've created several parallel copy-paste directories from the orginal \West Front and \East Front folders that were created by the JTCS install.

Now, something has gone wrong. Happened already before, when I copy-pasted a new Rising Sun folder, and put Warhorse's Korean Mod on top of the new Rising Sun folder (renamed it as 'RS Korean Mod' folder of course).

I noticed when I started a RS scenario, it saves the battle to Korean Mod folder instead? Also it must use some of the Korean Mod files, as the RS .bte I sent for PBEM was corrupt as far as the receiving party was concerned.

I booted RS both from the JTCS main menu, and by clicking the RS.exe at the RS folder. Same results.

Now the similar thing happened with my EF install, the EF started to save games into my parallel EF LWM1.0 folder, once I installed the latest LWM1.1 into vanilla EF with JSGME.

I recall reading W7 has a new file system, where physical files are no longer where they seem to be, but there is some virtual stuff on top of it. I recall especially older applications get confused by this.

Finally, my question:

Are there ways of doing a copy-paste that absolutely creates a new physical folder / directory structure? No virtual sh*t instead?

Or what's going on here...?