Message5228

I've confirmed that the exitfuncs are called but I've found that some 
unusual errors can occur during their call. This was due to the sys 
module being cleared via Py.setSystemState beforehand. For example I was 
able to print and call builtin functions in an atexit function, but 
import statements would mysteriously fail. This was all on trunk

I've solved that problem in r6851 -- I'm going to assume that was the 
issue you're hitting and close this out. Reopen if the problem persists