When viewing a profile as a guest my profile url displays as you would expect as seen here:
http://www.test.alpineascent.com/josh

But once you login in, the url translates to my user id instead. Here's the steps to replicate the issue on my site:

1. View any profile page. My profile is a good sampler page.

2. Click the login button at the upper right. Because this uses the popbox login, you will still be viewing my profile as you login.

3. The profile url will go from http://www.test.alpineascent.com/josh to http://www.test.alpineascent.com/62

It should still display the username instead of the user id for the url. Speaking of permalinks working with id's, couldn't this be potentially problematic if someone has a username that purely uses numbers bur someone else happens to have that id? Just bringing up another potential issue while we are on the permalink subject.