A related question explains this issue. drupal_find_theme_functions called on every page - is our theme registry being rebuilt?
With omega, there are 3 themes total (Alpha, Omega, and Subtheme) so this adds to the number of times drupal_find_theme_functions is called.
Shouldn't base hooks be stored in the cache? I see that it has logic to check to see if they are already set, but it seems like every time the page loads drupal_find_theme_functions calls preg_grep about 2,014 times. It takes 4,969,243 microseconds. I have a lot of modules installed, and this doesn't seem very efficient for every page load. Can someone please advise?
Looks like the issue is APC related, or at least I think so.
I installed APC and memcached previously to increase performance. I'm noticing some cached items are going missing even when they're set to not expire. I have features installed and tested features_get_info()'s cache which should never expire. It remains set for 5-10 minutes then goes away. Looking at apc.php shows 192M of 192M free about 500K usage, so something's definitely wrong. I'm not sure if the default APC/Memcache settings attempt to store the theme registry or not, but I'm going to play around with ttl values and see what works. If anyone can help, I'll mark this as answered.