I might be a little late to this post, but I have the same problem with pd-l2ork (version 2.5.1 edit: on OS X 10,12.6).
My Search Paths as well as my libraries and startupflags are completely blank, right after installation. I can't find the .plist files @maaark was talking about, can you maybe tell me where you found them?
Are there other fixes I could try?
(this is how it looks right now, shortly after the installation)
Maybe you know a fix, would love to hear it,