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I don't know whether this is a Media, Media Gallery or Chaos Tools issue.
With Clean URLs activated the normal Media Upload window (screenshot) appears additional to a second Media Browser window. If I click on "Abbrechen" (cancel) in the Media Browser the standard Media Upload window becomes visible.
If I click the x in the top right corner, the overlay disappears without reloading the page. If "Abbrechen" (cancel) is selected, the page takes me to the Homepage (starting page).
This problem disappears with deactivated Clean URLs. I was able to reproduce this error with a clean version of Drupal 7.20.
- Media - 7.x-2.0-unstable7+25-dev
- Media Gallery - 7.x-2.x-dev
- File Entity - 7.x-2.0-unstable7+39-dev
- Chaos tools - 7.x-1.2+44-dev
- Views - 7.x-3.5
- Colorbox - 7.x-2.3
- Libraries - 7.x-2.0