I think i just figured out what it is...
if you have the "Set it and forget it" option on in Diskeeper, this will defrag your computer every now and then, even while you are using it...

I noticed that while this is starting, this "freezing" appears to happen for about 4-5 seconds..

I tried turning it off, and it hasn't happened in a while, lets see how it goes

hope this helps,
Blackwar