It might be worth trying to use your Mac without running OnyX for a few weeks. Depending on your settings, running the tasks you mentioned erases large amounts of cached data in a wide variety of areas, which should have the effect of slowing down performance in many of those areas until the caches are repopulated.
If you're deleting the boot caches, starting up your Mac will take longer. If you're deleting the launch services database, opening different types of documents will take longer. Deleting application caches makes launching apps slower. And so on.
Ultimately, those caches are rebuilt, and at that point, performance in a given area should return to normal. But it sounds like you're ready to nuke them all again by about that time!There's no good reason to delete/rebuild most caches—after all, they're there for a reason—unless you're trying to address a specific problem for which such action is recommended.
If your issue persists through restarts and normal use, even if you're not running OnyX, then the problem is likely to be some kind of hardware or software corruption. But as long as you keep running OnyX as the first response to any issue, you're really making it more difficult to figure out what's going on.
