It sounds like some odd CSS is killing the cache mechanism that generates the CSS. Have you checked the log files?
Are you running Apache on Windows? Then add the following to your httpd.conf and restart:
<IfModule mpm_winnt_module>
ThreadStackSize 8388608
</IfModule>
Refs: https://github.com/bmbrands/theme_bootstrap/issues/342#issuecomment-58152495 - https://code.google.com/p/minify/issues/detail?id=62.
Also see this thread on the themes forum: https://moodle.org/mod/forum/discuss.php?d=271448.
