Interesting. Me and my friend were experiencing a similar issue - every 1 to 10 minutes, the game would freeze for 5 seconds and then resume.

He is on an SSD and I'm not. We didn't check the hard-drives, but we did notice that when we experience a freeze, the CPU would jump up to 100% and the GPU down to 0%.

I believe the issue started since hotfix #3.

Yesterday we managed to fix the freezing by disabling the Steam overlay for the game, and setting the exe files to 'run as administrator'.

I opened a thread about it here just a short while ago: http://forums.larian.com/ubbthreads.php?ubb=showflat&Number=701410#Post701410

Might be worth trying.

Best of luck!