K. Got it working
I edited app/AvrdudeUploader.java and added in the last function right before the commandDownloader.addAll
commandDownloader.Add("-F");
Now this will force uploading even for an improper ident which I would imagine could do bad things if you don't have the proper board hooked up.
The preference saving issues went away once I changed that.... very weird..... but good
I will write up another post that can be appended to the gentoo guide.