[Plugin: WordPress Automatic upgrade] backup archives empty and plugins not reactivated

My upgrade from 2.5 to 2.5.1 using the plugin went fine except for two issues:

1. The two back up archives I downloaded during the process were empty. I did a manual backup.

2. My plugins were not automatically re-activated.

Thank you for the plugin. It saved me an hour or two. I’m new to WP and I’m surprised that upgrades are so painful.