Seems when WordPress 2.5 (the self-hosted version) rolls out in a few days or weeks, who knows exactly when, the Automatic Plugins Upgrading feature will be pre-broken for your convenience.

Some WordPress plugins require that you uninstall them before doing any update so that they can properly remove any database entries and such that need to be removed before updating. At the very least, the plugin has to be deactivated prior to updating.

It’s seems the AutoMATTic code monkeys thought this was unnecessary bullsh*t to have to go though so they decided to ignore those things. Although in some instances, this approach may not cause any problems, there are certainly some plugins out there that will, if their upgrade procedure is not followed to the letter, turn your pride-and-joy blog to vapor. At the very least, it will require careful hacking of the database itself to get the vapor to condense back into something resembling what you had before, and few bloggers feel any level of comfort crawling into the bowels of MySQL. One slip of the mouse and the patient goes from the ICU to the morgue.

Another (if you needed another) reason not to be an early adopter of any software. 

[Edit 3/18/08 10:48pm MDT: According to WordPress Podcast, "WordPress 2.5 wasn't released last week as we expected, and don't expect it for several weeks." Perhaps the above problem will get some attention during that time.]