I also have a problem after customer logs in. As they go to checkout, they get an extra page before FEC that says Shipping Method and has shipping method special instructions. After you press continue checkout...go to real FEC checkout page.

Breadcrumb shows:
Home > Checkout > Shipping Method
then hit continue checkout button at bottom of page and
Breadcrumb shows:
Home > Checkout
This shows the one page FEC with confirm order at bottom of page
Then takes you to extra confirmation page that stays for one or two seconds before Paypal.

Does this make sense?

Thanks, Kim