Maybe removing Mail.app from the list and readding it may help?
There have been reports of Upgrade and Archive + Install having a few bugs. Like, dragging QT from the dock and back into the dock and iChat the same will 'upgrade' the icon.
Didn't have the dock problem (cleared caches before updating) and de-adding it and then readding it doesn't work. Are there people without this problem?
Oops, I didn't see all the other posts. Hiddenmail is still available so I'll try it. Would still like to know if anyone has heard if this is on Apple's radar to fix. I'm guessing not, since nothing's changed in 3 years.
Well HiddenMail seemed like it was going to work, the blue ball appeared under the mail icon on the dock and the HiddenMail icon disappeared but then Mail opened anyway even though I had taken it out of my login list.