So MC remains responsive, works, you can navigate and play things, but OSX "thinks" it is busy and is showing the beach ball?
I've actually seen this occasionally with MC as well. Though certainly NOT every time I touch anything. More of a once in a blue moon I have a vague recollection of seeing that, but quitting and relaunching MC (or maybe, worst-case, rebooting) made short work of it.
I'm not sure at all how to solve it, but actually it happening all the time is a pretty good way to maybe get closer.
Can you make it happen, do some stuff, and then gather a log package and post it? If it is too big to attach (probably) you can use a service like Dropbox or WikiSend to make a temporary URL and then post that.
Also, do you have anything weird about your Library? Any funky customized views? Or things you struggled with setting up a Smartlist, expresson column, search or anything else? Maybe any weird settings or hardware?
Thanks.