In the last couple of weeks, we've had a few users ask questions pertaining to installing Drupal Commerce on a site updated from Drupal 6. The sites in question weren't Ubercart migrations, so there was no e-commerce data to bring forward. That's where you'd usually expect hangups to occur, which is why we're devoted significant time to the Commerce Migrate module to help transfer data from an Ubercart site into Drupal Commerce.
Instead what often gets in the way is the change in approach from Input formats on Drupal 6 to Text formats on Drupal 7. If I remember right, the issue is that Drupal 6 uses serial numeric keys for input formats but Drupal 7 supports machine-name type naming of text formats. During the update process, it appears that the numeric key for an input format becomes the machine-name for the text format on Drupal 7. Not a huge deal in and of itself, as everything in the site will still be referencing that same name.
The problem comes in on the checkout completion message in Drupal Commerce. We allow for text format selection in the settings form to configure the basic message, and we accommodate two core text format names we know about. If it is available, the message defaults to the Full HTML format, because we expect that to be created in a Standard installation of Drupal. If that isn't available, we fall back to Plain text