This problem started cropping up since WordPress was moved to version 2.5. The plugin worked just fine in previous versions.
What happens is that the whole upgrade process moves normally. I upgrade the database and all, and then I try to reactivate my plugins. At this point I will always be taken to the login screen as if my cookie had suddently expired. After I login, I am taken to the WPAU page where I am asked if "I am certain I want to do this" (or somesuch, can't remember the exact message). I click the "try again" option but it will just return me to that screen.
In the end, all the plugins are left disabled, except WPAU. and I have to manually activate all of them. This wouldn't be a big issue if I didn's have close to 30 plugins :-/
Since I run multiple WP sites, I tried another thing. When the "activate plugins" step arrived, I open a new tab to my admin page and logged in from there (just to get the cookie). Unfortunately this did not help as when clicking to reactivate the plugins I was taken to the same "Are you sure" screen again.
I assumed this might be related to the change from 2.3 to 2.5 but when trying to move from 2.5 to 2.5.1, the same problem appeared.