Well I found a fix I disabled SEF url's for the cart which seems to be working ok. For some reason
the cart not SEF url would use the index/register SEF if you decided to leave checkout to browse more products. Once you tried to 'show cart' this would load the home page and my customers could not checkout. Also leading to a loop.
I had "Set server QUERY_STRING?" option to "Yes".
Disabling SEFs for the cart, deleting all the 301 redirects and redoing as needed and disabled SEFs on User seems to have fixed the problem and site runs smoother and quicker.
With all the problems I have had with Sh404sef and now Joomsef sometimes I wonder if it's worth using SEF for URL's.