check your midi signals with this midi monitor app (it's free):
http://www.snoize.com/MIDIMonitor/
then, at least you will know whether the glitch is on the logic side or the pd side.
if it's on the logic side, then focus on that to see if you can find the error. As i said, i highly doubt logic has any serious bugs like the piano roll not working; but there might be some setting that is not obvious, or something like that. You're probably not the only one to encounter such a problem, so have a google.
Sometimes cracked software has weird glitches though, and of course no one here would use anything like that (cough), but that could be a possibility.
Unless the problem is with pd, though, not sure how much help any of us lot will be.