Julie,
For 32 bit systems you should use the 3.3.5 version.
It sees all of my pins. There is a bug in the 64 bit version <Also 3.3.5 > that is giving the pins files trouble. Mike is aware and will be addressing it soon.
See my screens below If you click ok on the error dialog the CM program will still run but the pins are certainly an issue...I'll see what I can figure out..
Greg