This doesn't need help - I figured it out myself. Hopefully it will show up in a search if anyone else has this (heartbreaking) problem.
I would make a project in several different versions of Quartus II, create a processor in SOPC builder, compile it all, load it into a DE1/DE2 board, then run a nios2 project based on the hello world template, and all would be fine and dandy. BUT, if I tried to run a nios2 project with microC running, I would get the following error when I tried to build it:
**** Build of configuration Debug for project hello_ucosii_0 ****
make -s all includes
Creating generated_app.mk...
Creating system.h...
Jul 24, 2009 11:32:53 AM - (SEVERE) generate: java.lang.IllegalStateException: java.lang.IllegalStateException: java.lang.NumberFormatException: empty String
make[1]: *** [system_description/../obj/system.h-t] Error 1
make: *** [system_project] Error 2
Build completed in 29.842 seconds
Very frustrating, but eventually I discovered that you can fix this problem by putting a timer module (in a similar category to PIOs in SOPC builder) in your SOPC system where there wasn't one before (ideally, put one in in the first place...)! Then, new projects with microC will work fine, and old projects with the above error should work fine once you go: Project -> Properties, Associated System Library, System Library Properties, and set the System Clock Timer to the timer in your processor.
