Oh yeah. I did. I've seen this problem posted by others with no real solution either. The only conclusive thing to do is to edit the template outside of the Auctiva editor and copy and paste it back. Then so a save without touching it.
The editors in Auctiva are weird, to say the least. They apparently can only deal with simple code. If you bring something in from Frontpage, for example, even a simple page layout, there will be something in there that jacks up the Auctiva editor.
So I guess the only real solution is to either do as I said earlier and don't try to change it in Auctiva or create your template from scratch within Auctiva. Either way it can be a pain.