I decided I had to take a look at patching the X-Linux system with a real time patch which should be more suitable for the control system. The system is currently running very well, very little jitter, but it would be nice to remove possible kernel interruptions! I have been putting this off, as I have no idea where to start, however, I followed the how-to on this site: http://rt.wiki.kernel.org/index.php and after half a day I was able to patch and re-compile the kernel and install it on the HexEngine target :) well pleased! This also means that I am also able to add and remove features to the X-Linux system such as wireless internet drivers, FTDI serial drivers etc and remove unwanted stuff such as audio driver that may be slowing boot time. This has ticked off a major issue for me that has been lurking in the back of my mind, I'm sure this is childs play to a linux guru, but to me it is good progress.
One problem with the patch so far is that the Vortex86DX does not seem to support high resolution timers, so my jiffy time is still 4ms (250Hz). However the real time patch has seemed to improve jitter.