Hi,
I had the same bug one year later, I think with vanilla... IO gave me a hack on this list, but then it seemed to be resolved as I installed PD-extended... but that bug has just returned...
The solution was to launch pd with:

$ pd -alsamidi -mididev 1,1

the old topic is here:
http://www.mail-archive.com/pd-list@iem.at/msg30157.html
I'll try it tomorrow and report...
but if anybody knows what the problem is...

how did it disappeared for you?

cheers
raf