I've just installed a fresh Drupal 6.8 with the latest UberCart (6.x-2.x-dev). Site Documentation reports:

# 'Shipping Quotes' for the 'Ubercart - core (optional)' package was found in 'sites/all/modules/ubercart/shipping/ ' but a previous module was in 'sites/all/modules/ubercart/payment/ '.
# 'Shipping' for the 'Ubercart - core (optional)' package was found in 'sites/all/modules/ubercart/shipping/ ' but a previous module was in 'sites/all/modules/ubercart/payment/ '.

Except neither of those modules seem to exist in the payment directory.