Pay close attention and you might note that animations are also slowed down with the run speed. If that's the case, I also get this issue on one of my Windows boxes -- never been able to resolve it (although there are a multitude of alleged solutions for Windows).
Sometimes it runs full speed, sometimes it seems like full speed but i'm actually at 90% speed and mobs will be able to catch me, sometimes it drops to like 50% speed and attack animations look comically silly. The spell cast meter also acts funny when this is happening (if at 50% speed, the spell will go off when the cast bar is only halfway done going down). Runspeed and character animations scale with it, but framerate stays the same.
Supposedly solutions to do with specifying the priority and cores used by the program have helped some people. I can't really remember the specifics because I was never able to get results, but they're on this forum somewhere.
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