I have investigated the problem and it turns out virtualenv patches distutils.sysconfig behavior by adding to the sys module a "real_prefix" attribute that points to the global Python install and is used instead of sys.prefix that points to the virtualenv local install, when some distutils.sysconfig APIs are used.

The fix is to change virtualenv so it patches sysconfig the same way it does for distutils.sysconfig.

To simulate this patch, just change how _EXEC_PREFIX and _PREFIX are set in sysconfig, by setting them to sys.real_prefix instead of sys.prefix/sys.exec_prefix when using virtualenv. 

I suggest to Georg that this bug gets resolved to "invalid" and that we move it to the virtualenv bitbucket tracker.