Thanks for your reply, Libor. I will have to edit my post -- I did try running the build from KDS, and I do not get any errors there. It compiles and links great. It's just the headless build that doesn't work. On another build server with the same versions of KDS/Eclipse components, headless builds work fine. I'll double check the KSDK preferences, though.
I had inquired in a different post about quieting UI dialogs -- thank you for mentioning this! However, I am of the mindset now that having the build freeze on me is okay, as this implies that there's something wrong going on.
Here are my KSDK and Processor Expert preferences:


This is the command line string used for generating the PEx code:
c:\Freescale\KDS_3.0.0\eclipse\eclipsec.exe -noSplash -data C:\MyProjectFolder -application com.freescale.processorexpert.core.PExApplication -generate MyProjectName