Many Thanks 
After much digging, i came across a copy of MB extension 2. I have tried the Biped template, and it’s hit and miss.
I had one modified biped character, and using the template, marker sets, and .fbx format for everything it worked fine. My pipeline was as follows:
Create biped > Export as fbx > Open in MB 7.5 exp 2 > characterise with the template > import .trc, and set-up on an actor as normal; then have the biped skeleton follow the actor stance > plot to the biped > Select all the biped components only and export as a Kaydara file (.fbx, animation only) > import the kaydara fbx to the original biped in the file which I exported from.
Up until now this worked a treat, but I just had a go with a new character, who isn’t even a modified biped, followed exactly the same principle, and no animation is coming through the import to max at the end, it’s as if I had forgotten to plot to the skeleton, but I haven’t.
I’ll give this bvh a whirl as hopefully that will fix it, many thanks for linking it, my Final Year Project is kind of hanging in the balance.
The only thing that is different is the amount of frames in the file that wouldn’t import properly.
Over the slider in MB, it gives the message ‘Too many keys for edit’ when I have any part of the skeleton highlighted. This is the only thing I can assume is disrupting what was a fuctioning workflow.
Either way, hopefully I won’t struggle to much with this .bvh stuff now, much appreciate you taking the time to link that for me Annakey 
EDIT: to answer your question on what the biped template is for, so far as I can tell, it just allows for automatic characterising of a biped skeleton so that it works properly. It allows any of the structure options that biped in max gives you to work as well, and sticks them all in the right slots.
Kinda handy for folks in a similar situation to me, who are trying to get Mocap into max via biped with relatively little blood or sweat. I don’t know if it has any further options as I have only used MB for Mocap transfer, and not for proper hand animation yet.