I am making some larger scrolls on the scroll jigs I made.The scrolls are 8"-12" in diameter and porbobly use 24"-36" of stock. I have used the jigs quite a bit for smaller scrolls and had no trouble. I notice that when I take a nice long heat, to get as much of the scroll formed as possible that the square bar (1/2") wants to twist. This only seems to happen when the stock I a scrolling is long (6') as the shorter ones seem to come out without the twist. I am wondering if I am taking too long a heat and my right hand bias is coming out, but the shorter heats it is not apparent.
Any ideas on this would be great as I have about a dozen more of this size to make.

It is entirely possible that it is twisting with the longer stock. I can take about 12" of usable heat in my propane forge and usually get that much to successfully follow the scroll. However, square stock usually doesn't have this problem so is it possible your form is twisted to some degree? Another trick is to keep the scroll flat as you go - every time you take a heat and scroll, go to the anvil or (better) your layout table to true it.

You might also want to use a torch and simply follow the form with localized heat.

When bending square stock (or any other), it's going to want to follow its "easy way" unless you persuade it otherwise. For square stock, the easy way is to bend on the diamond instead of on the flat. (If you just take a piece of light square, say 1/4 inch, and bend it cold around your knee, it will go on the diamond every time.) As noted, you may have to heat and bend in smaller sections so you can apply correction as you go.