I just switched user accounts at the advice of Apple and now when I compose an email and then go to the drop down and choose another account, I get the HTML signature for the default account first and the selected account second.
With the sad state of Applecare now (at least by phone) I can't get an answer to save my life.
One more issue that keeps happening that they can't seem to solve. Some of my accounts periodically go offline, showing that warning triangle. But when I click on "show account info" and let the info show, they go back online.
The final issue is that Apple mail drops my passwords on a regular and random basis, making me put them back in manually. I've repaired the keychain and it didn't help at all.
If anyone has solutions to these issues it would be very much appreciated. It's a sad shame that Apple doesn't!