Are you sure that no folders related to the installed games are open in windows explorer? ... try closing everything except this before switching.
Did you unfortunately install Oblivion in the default location on Win7 or Vista? Although related to Wrye Bash http://www.uesp.net/wiki/Tes4Mod:Wrye_Bash/Installation#Windows_Vista a bit about why that can be a problem.
Otherwise I can bet for Gaticus to diagnose your issues he will need to know where each clone is installed and on what operating system.
Kia Ora
my bad your so right, I shouldn't treat you all like mind readers lol
Win 7 64 bit and the game path is:
G:\Games\Bethesda Softworks\Oblivion
G:\Games\Bethesda Softworks\Mesogea
G:\Games\Bethesda Softworks\Nehrim
G:\Games\Bethesda Softworks\Middle Earth
G:\Games\Bethesda Softworks\Oblivion For Modding
G:\Games\Bethesda Softworks\Oblivion For Playing
That way I can check out the conversion mods without messing with my game or mods my mTES$ is v0.5.1b