If you have multiple versions of Windows installed on your computer and you wish to hide your folders for all versions then you'll need to install Magic Folders for each version. In other words, boot to each version of Windows and run MFX.EXE (if Win2K/XP).
If you have Windows 95/98/ME installed then you'll need a different version of Magic Folders which you can get at http://pc-magic.com/mfd.exe After installing the Win95/98/ME version make sure you hide the C:\x___x folder as that folder contains important info for the Win2K/XP version of Magic Folders.
I'm sorry but Magic Folders is not available for NT 4.0 or before.
The encryption method used by the Win95/98/ME version of EMF is completely different than that used by this version. Files encrypted in one version will not be decrypted in the other. If you have encrypted files in Win95/98/ME you will NOT be able to use them in this version, and vice versa. You can hide the encrypted files on another OS but don't encrypt them or they'll be unusable in both OSs (until you remove the encryption).
In other words, if you have EMF encrypted files installed in Win95/98/ME you will not be able to use them in Win2K/XP, and you should not encrypt them with this version or they will be unusable in Win95/98/ME. If you want to use the files in both versions of Windows then remove all encryption and just hide them.