Hi,
I recently upgraded from Drupal 5.12 to 6.6 and now I'm unable to rearrange block order. I click and drag blocks to where I want them, and as soon as I save it reverts back to the way it was.
We've had some problems with the themes not being explicitly enabled on (among others) D5->D6 sites: when you go into themes, the radio button for the current one is selected, but none of the checkboxes are! However, this gives us a weird perms error on the Blocks page, rather than simply failing silently. But check the theme you want to use is definitely enabled.
Cheers, J-P