It looks like that W3 Total Cache cleans the op code cache in random times. Using apc.php i noticed that User Cache Information keeps growing to ~30MB but usually purges around 4000 files. The trigger caused but different admin behavior susch as saving settings etc. Disabling cache for admins helped a lot but still the problem persists.
Note that APC has 256MB or RAM and only ~30MB go to User Cache Information and W3 Total Cache. Approximately ~40MB are File Cache Information which are *never* purged randomly. For the sake of figuring out what's going on, i set very high TTL times on W3 Total Cache which are confirmed on APC stats. W3TC is configured for page, database and object cache only.
Purging and building the cache all over again causes unnecessary load on top of the daily load. I can't figure out why W3 Total Cache behaves like this. Is it normal to have the User Cache purged when clicking on the Admin > Comments menu to see the comments? Because this is happening.
Latest version of W3TC, WordPress, APC used