Qsys IP Search Path disappears

Okay, I figured this one out.

I installed Quartus on this machine to the /opt directory using sudo. It created a .altera.quartus file at my user root directory but it was owned by root and part of the root group, thus I didn't have permissions to write to the files in that directory. Quartus must use the quartus2.ini and quartus2.qreg files in that directory to store state information.

I chown'd the folder and files and the problem is solved.