Just above the LHO square there is a little faded grey colored circle like a timer with a yellow bar protruding from it that goes around the circle like a clock hand almost it takes about a minute to go around and then the middle of the circle turns gold for like a second anyone know what this does??

I think it is a part of the regen counter. The counter counts a minute when it reaches top (00.00)

it's some sort of "refreshing" counter. You might have noticed that you don't loose ap and ve instantly when you lose then, they only get updated when you refresh magicduel (F5) or when that little golden bar that runs around that circle reaches it's top position and it glows for a moment.
If you don't believe this, try it out, walk around a bit and look at your ap, they get updated when the circle glows^^

ps: that thing doesn't always take a minute to make a full turn, it has funny intervalls sometimes

Thanks guys. I asked around but nobody was sure what its was for.