Evan,
What your finding here are elements and attributes that the Mozilla validator doesn't know anything about. A great example is the dojotype attribute. This is specific to dojo, and the validator doesn't have dojo validation built in.
The way I work around this in Aptana is to put all of my javascript code into individual files in my application folder structure and just reference the file in the HTML. This way, when I'm looking at the javascript in Aptana, there is just javascript, and I can trust what I see in the validation window. If I look at the HTML in Aptana, I just pay no attention to anything in the validation window, as there's no javascript there.
I would recommend switching your validator to the jslint validation in Aptana. I find JSLint to be more complete and offer better warnings. The fact that you're using any validation at all is kudos to you. Your apps will run much more reliably and with better performance if you take care of all the little code details.
Jeff