Thought i'd update this, as i have it all working now. I'd tried all the usual stuff like checking individual components. voltages, shorts etc.. I'd also flashed the bios to the latest version, although i'd already had that version. I ended up flashing to the previous bios release and all is good now. As my system is practically always on, i've probably had this problem for a long time, as i do recall odd occasions of boot problems. Anyway, i've tried multiple boot scenarios and all is well with this version of the bios http://downloadcenter.intel.com/Detail_Desc.aspx?agr=Y&DwnldID=17198&ProdId=2864&lang=eng. It's slower to boot but it was always like this with this release.. At least it works! Hope this may be of help to someone with a similar problem.
If there's any change i'll update this page.