D'oh, my bad, you're right. I re-installed MCPC+ and they are working now.
In other news, now that I have that working, I ran into an error that I'm not sure if anyone else reported yet: Phase pipes. If you break a pipe connected to a phase pipe, it crashes the server. In order to remove pipes connected to a phase pipe, you must first break the phase pipe, then remove the connecting pipe, then put the two back together.
Crash log here:
http://pastebin.com/j7zhciJF