Under the Messages Build Log you should see a msg like "Executing .." xterm or whatever.
What does it say it's trying to do. Anything?
Mine: SVN 3676 shows:
Checking for existence: /home/pecan/proj/conio/conio
Executing: xterm -font -*-*-*-*-*-*-20-*-*-*-*-*-*-* -T 'conio' -e 'LD_LIBRARY_PATH=.:$LD_LIBRARY_PATH /home/pecan/devel/trunk/src/devel/cb_console_runner "/home/pecan/proj/conio/conio" ' (in /home/pecan/proj/conio/.)
There's recently been a "War on Macros" that's kinda messed a few things up. You might want to revert to an earlier SVN (like above) if you want to execute or debug from Linux.
Eventually, the "War" will end, and it'll all work again.