I'm having the same sort of issue - Windows 7 64-bit, MatLab 64-bit. I tried to run the program on another computer, a Win XP 32-bit, but the MCR could not be installed. The solution I'm working on implementing is to install MatLab 32-bit, and therefore the 32-bit MCR. I'm hoping this will solve the problem.
However, is there a way to instal multiple MCRs in the same bundle? Or do you have to instal the MCR manually on each computer you wish to run the program?