Intermittent stoppages whilst playing a file

Hi all..
just upgraded my DAW from win 32 to win 64 and upgraded HS6 to X3 studio.
 
After a lot of work, all seemed to be well with VSTs installed again etc and the  Behringer FCA1616 I/O sorted, however I am now experiencing brief stoppages whilst a file is playing. The whole track stops for about half a second - no audio from my midi driven outboard boxes and the VSTs all stop as well. It then starts again - from the exact point it left off.
 
Obviously I'm still working my way around x3 so my experience level is still low at the point, but is this a program fault or a PC fault? Maybe I need to re-install X3 again?
 
Occasionally I also get a very noisey VST output whilst playing a VST from my controller keyboard.
 
Any advice welcome

Hi there and thanks for the info. I've tried a few other settings but can't get to be reliable enough for some reason. I've decided to try a new Focusrite Saffire pro 40 as a replacement anhd see if that holds up better.
Your links look interesting too, I'll give them a look.
 
Mike
 

Hi Anderton...
It starts again on its own - doesn't need any help from me. Tne track stops and starts on the screen exactly in sync with the audio too.
I've replaced the Behringer with the Focusrite Sapphire 40 and so far that seems to have sorted it out, but I still get a continuos low level cyclical burst of noise every 3 seconds, lasting about 300mS. With no tracks audible it is really annoying. Once track audio is "audible", it's not noticeable, but I'd like to know what's causing it.
 
As an excercise, I've used my M-Audio Firewire 410 as the A/D interface and its' just the same, so something in the PC doing it or the Firewire interface in the PC perhaps??