I'm curious why anyone would think that reducing load on a CPU would be a bad thing - i.e. turning off HW Accel on any card - why would you spend £££'s on a card with Gigs of memory and a super fast GPU - then do the some of the video processing in a CPU is just plain crazy.
I've had many issues with stutter, delays and hangs but all have been eliminated over time and were a variety of search indexing, background process's, refresh rates, driver versions and outright interference by the operating system, even AV amplifier issues.
What is your playback chain ??
I know this is going to upset some but have you tried things like Media Player via Shark 007 Codecs - does it behave the same - have you checked out what your CPU is doing at the time, does it do it when windowed or only when full screen etc? I guess what I'm saying is does the behaviour exist in other players / codec / playback chains?