IF I remember correctly the drive that the clone goes to. Has a differnt drive letter than that of the origional (EX: Origional was C:\ Cloned is E:\)
And that is still the case on boot from that HDD then the problem could be when you installed the program it mapped as if it were working out of C:\ and now that it is in E:\ it doesn't know where to find the required files.
If I had to guess I would look at that first, but then again I can't see the problem do its just an idea tossed out there.
And yeah if its not freeware and you did not purchase it legally that could cause a problem
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