Actually I used both StormC and vbcc, but the main part (libraries, startup code, etc.. ) are from StormC.
I own an A4000T but It was tested on both A4000 and A1200.
As another user suggested, you need to delete all the old .ms2 files from the ID1/glquake directory.
It doesn't support skyboxes atm (these works with blitzquake)
Ciao
Massimiliano Tretene, S o f t 3