In the Additional Options section when generating, select Apply to all Topics and then select the CSS and Master Page you want. Try that avenue.
Just tried that out.
With no success unfortunately. Thanks though, didnt know that option existed - may be useful in the future.
No I looked at the code and it seems to be ok with head and body tags where they were supposed to be.
I gave up in the end and have created a new master page and reattached it. Bit annoying.