Heh nothing like posting answers to myself.
Anyway, fixed it. Was a setting THORUI put in with its custom set up on speaker set ups. Should be surround and wasn't. I had clicked one of its custom set ups and I guess that changed my speaker set up.
Might keep a note of this for others, going to reinstall now.
Finally got rid of all elements of it too, was not easy!
But I like the UI so going again to see if I can now get it working right.
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