I have a feeling it was something other than the fact one was PCM and one was FM. But, hey, I've been wrong before!
I have a 9C and can use my buddy box on either PCM or PPM.
The main difference between PCM and PPM (they are both FM signal transmissions) is that with PCM, you can set the plane's servos to go to a predetermined position. This way, if the signal is lost you know what the plane will do.
For example, you have it set to go to idle, a little up elevator and a little right aileron. Now, if you are inverted when it loses the signal, it doesn't really do what you might like. The throttle down feature is nice, though. That way you know it's not going to go full throttle into the ground or ??
With PPM, you have no idea what the servos will do. I've heard PCM is more resistant to getting hit.
Hope this is helping some.