Hi,
Well... MSM can't be installed by dropping a cloned drive into a PC - it's a real program, has multiple libraries it uses (not all of which live in the mach folder), for these reasons MSM comes complete with an installer etc.
Do this:
1) Run the MSM installer. Reinstall the same MSM version - just let it install on top of itself. That will get all the bits & pieces into the proper places. No need to create new profiles etc - the existing ones will do fine.
2) Reactivate MSM (ref page, activation button. Online activation is the easiest and fastest method). That will have MSM go talk to the license server and then all will (probably) be fine (I'm betting that you reverted to a clone HDD due to some hardware failure.. so MSM will probably think this PC is different from the prior PC).
If any issues crop up, let me know.
Dave