Unfortunately this is a quirk of Toyota's Navigation system. Not entirely sure why they designed it like this, but they did.
When the Navigation Head Unit loads up, if is unable to read the disc (be it the disc being bad or the head unit being bad) it will not load into any other function until the disc read error is corrected; which in my opinion was a poor programming choice on Toyota's part.
Unfortunately the bad new doesn't stop there, a lot of times we've seen that it's either the disc or the head unit. I would see if you can make a DvD from your current gen map software (for diagnostic purposes I would try not to use an updated disc as they overwrite the data on the head unit and won't want to use older discs in a lot of our systems) this way you can rule out the DvD being the issue.
If you can't get one or make one, you can try sticking a plain music CD in the map slot and starting the vehicle up. The error should change to something along the lines of "incorrect format," this way you can see whether or not the head unit is even looking at the disc. I've had a few dead units that didn't even bother responding with a different disc or CD and we had to replace the entire unit.