Hey! Am I too late to help?
I'm having a similar situation, and it seems to be cause by the Novation Xiosynth.
All my other MIDI devices work (well, I only have 2 others - a Korg nanoKontrol, and a Behringer BCR2000), and Xiosynth shows up in other programs just fine. But whenever the Xiosynth is plugged in to the USB port, PD can't open its MIDI dialogs.
Xiosynth WILL show up as an output option under "audio settings," but PD just crashes when I try to open MIDI settings.
So, on my OS 10.5.8, I deleted the following files, from my Users/"my_name"/Library/Preferences:
org.puredata.pdextended.pd-gui.plist
org.puredata.pdextended.plist
org.puredata.pd.wish.plist
it MAY be that only the last one needed deleting. In fact, to be safe, I've just been moving them into holder folders, in case I need to put them back - I don't know what does what, so I'm being cautious.
Strange: XioSynth worked with my Ubuntu PD without issue (probably an older build?), and XioSynth works on other programs on this Mac. But it crashes PD so hard-core that I need to delete those working files.