A quick update on this story... I finally brought it in to the dealership for the next oil change and to have them look at the navi bug I was experiencing. They test drove the car, did what I described and verified the malfunction.
Their first response was, ok there is a TSB for the navi to replace the antenna bracket and a new SD card. Ummm... well I pointed out that this TSB was performed months ago on my car to fix other Navi issues I had experienced, which didn't fix it (and for all I know, could have caused it). So the next move now is they have ordered an entirely new Navi unit which should come in about a week. I was a little surprised that is the solution, not some kind of simple software update. So I guess I am getting a new head unit.
Will advise when it is done and whether that solves the issue.