this seems to be due to the top-level import of ctypes in webkitpy.common.system.executive.py, which is only needed on win32. I don't know what ctypes is doing to cause the problem, or why it is only happening in config_standalone.
Created attachment 153108 [details] Patch
to reproduce you can run 'python config_standalone.py --mock Debug' from the cygwin command prompt, and you should see "Debug\nAborted" with python crashing at process exit :(. You of course may not be able to reproduce this, as it doesn't seem to happen on the bots.
Comment on attachment 153108 [details] Patch Too bad we can't use the win32api module instead. Ah, the joys of Cygwin!
Comment on attachment 153108 [details] Patch Clearing flags on attachment: 153108 Committed r123133: <http://trac.webkit.org/changeset/123133>
All reviewed patches have been landed. Closing bug.