Betty - it all looks fine (although I will say that the files in both my 1.3.8 and 1.3.9 directories are 644 permissions).

One additional quick question - silly, but have to check and make sure. The qbms module will show up at the bottom of the list as "Pay by Credit Card" with only the second column showing "qbms". Are you sure that's not at the bottom of the admin payment module screen?