I have posted about this problem before, however, since the WordPress Automatic Plugin Updates (WPAU) have been working there is a new culprit for this bug. It appears to be somewhat of a random bug that occurs when you run an automatic upgrade on a plugin.
To catch this bug before it causes an unexpected problem you should check each plugin immediately after running an upgrade. Simply click the Edit button next to Deactivate, scroll to the very bottom of the file and make sure there is no whitespace at the end of the file. If there is whitespace, simply delete it, and save the plugin. See example images
If you do not check your plugins this bug can become a real pain. The main reason is that once it occurs you have no idea if it is in the WordPress PHP, Plugins or Theme files.
I just ran the my first set of WordPress 2.5 upgrades.
The first upgrade was to a very small blog with only 2 plugins, the second was to a larger blog that had several plugins installed. Both upgrades went smooth as silk.
The WordPress 2.5 dashboard and layout are totally different from anything WordPress has released before and it will take some getting used to. I did use the upgrade automatically option on a couple of the plugins and everything worked as expected.
One new feature I really like is the Tag management. As an example I had a tag that should have had a word capitalized that was not. I was able to modify the tag display with a couple clicks and then verify that it was corrected in my tag cloud.
So far WordPress 2.5 looks great and I will follow up with more data as I upgrade the rest of my blogs.