Looks rather like a problem with your system setup. Especially if your self compiled pd works, the debian package should work too, its the same code.
If it really behaves differently, I would be very interested to find out why.
if you build pd yourself on debian, it installs /usr/local/ instead of /usr or so..and grab the gui from one path, and the core from another...one being from the .deb and one from your custom build...and crash on launch, etc. at least i think thats what was happening.. anyawys i just symlinked /usr/local/pd to /usr/lib/pd so it couldnt happen again..