First off put a cd\ before that second cd ..... some versions of windows don't care for switching paths before going back to root.
Secondly, you don't have any wait commands in there, just a timeout command, which probably isn't what you want.
You want it more like:
start /wait rtpMIDI.exe
As for the 64bit question, I don't think I understand. Why can't you call protools 10 after protools 11? They are in different paths so even if the exe name is the same it shouldn't matter right?