paste your compile log here for a list of errors i can spot 3 atm http://www.interlopers.net/errors/
This is a fatal error, which prevents a new BSP file from being written. Most likely, this overlay is too large and/or it is applied to a brush face with a low lightmap scale.
pretty much what 03C0 said. Also the overlay may be applied to a brush that is large, try breaking it up.