Was Drupal already installed there at one point? There will be problems / inconsistencies if you removed old installation files but didn't empty out the previous database. Does this make sense?

Thats my guess as to why the modules would've been enabled already, but I could be wrong.

Check your watchdog (error logs) and see if it's saying anything. If it isn't I think you're okay. Thoroughly test the checkout / shipping quotes procedure and report back if you have further issues. Sorry you didn't have the easiest experience so far.