Thanks to Tom, a PDX Bus user, we have worked out why the trip planner doesn't work sometimes, and how to fix it until I get a new version out to Apple.
If you are getting odd results, it is probably because the "Maximum Walking Distance" has been clobbered with an invalid value. The biggest this should be is 2.0 miles, so if yours says 5.0 miles, then PDX Bus will have a problem.
The fix is easy...
From the iPhone home screen choose Settings, then scroll down to where it says "PDXBus".
Scroll down to where it says "Max walking distance", and tap that to choose something (such as 0.5 miles).
That's it!
The trip planner will work much better with the proper value. Thanks for your patience and thanks to Tom for his help!