Open it up to see the guts,someone dorked with it I'm sure.
This.
Especially if running the Class 5 using your Traynor's speaker doesn't help.
If you look at the length of this thread (which a couple of other folks mentioned in earlier posts as well)...
http://www.mylespaul.com/forums/squawk-box/123816-some-mods-marshall-class-5-a.html ... you get the sense that there are a lot of modded Class 5's out there. Maybe there was something done to this one that wasn't quite right. (Part of the reason that thread went so long is because some folks initially misfired doing the mods themselves.)
Or it could be, as tuckermde suggested earlier, something in the stock electronics is just not right.
Regardless, I think it'd make sense to have a tech that you trust go over the thing to try to figure out what's wrong.
For what it's worth, I now own both the combo (which has had most of the afore-mentioned mods done to it) and the head (which is in the shop having the same mods done to it). The Class 5 is kind of a one trick pony, and I only use it for crunch tones (I switch to another amp entirely for cleans).
And yeah, the combo sounded better after I changed out the stock tubes and had the mods done to it. But both it and the head sounded pretty good stock, certainly not muddy.
And yeah, both it and the head sound better through a beefier cab / speaker setup, but I still gig the combo with the stock 10" Celestion...
I really do hope you get our issue figured out.