Thanks for the reply,
I've uninstalled everything and re-installed PMS. Now the video plays fine without transcoding and goto works. I have also verified this with another video (again a .m2ts with H.264 and AC3) and again the goto function works.
My problem now is that if I play a file that needs transcoding (the example file I am using is again a .m2ts but this time with VC-1 video and DTS audio) the goto function no longer works correctly (it will only skip ahead a couple of minutes no matter how far ahead I set in the goto options).
Again I'm not sure what could be causing this, and it is my only major gripe, so any help would be appreciated.#
Should I try install a codec pack? I'm not sure if this will have any impact in that it won't be used with Mencoder.
p.s do I win a prize for saying "again" the most times in one post