Hi,
Please, try rtcw with Windows 7 if you can. I compiled very large sp maps with Windows 7/gtkradiant 1.4/q3map2 1.6/EasyGen 1.42 and got no shader overflow bug. The bug was though visible under Windows XP.
Pay attention to install q3map2 as instructed. Its DLLs are not compatible with the standard gtkradiant 1.4 DLLs.
Good luck.