I recently upgraded to PHP 5.3.27 so maybe it's related to this. I had some errors about timezone settings, but I corrected this with the timezone set in php.ini. I have no other errors in the log.
If I edit a menu item and set the weight, it works. If I set the weight from the DB, it works. The only thing that doesn't work is the rearranging on the items list page.
Edit: PHP log shows no errors even with E_ALL reporting. I think the problem is with Drupal, as it only lets weights from -50 to 50 and the rearranging can't put the items where I want them. Whe I set weights of more than 50 in DB, the ordering was correct, just until I wanted to change the order withhin Drupal. Then, the manually set items scrambled. Is there a way I can set it up to allow values in a wider range? I don't want to rearrange everything via DB it's a pain in the ass.