I had the same issue with the system and the 3GS but it has not happened since I did this
I wonder if the following would help, there are reports that it updates Bluetooth as well, probably meaning new phones as they come to market maintaining compatibility!
For UK owners at least there is a software update for our units which fixes the Bluetooth issue of only displaying the first track on your device and more importantly switches on traffic updates in the satnav system.
I presume that there are other upgrades and patches too, I need to research more to see what they are.
I have just downloaded and installed in the i40, a pretty painless process, but don't believe the bit on the site where it says insert the USB drive and the update will take a couple of minutes, it's more like 20 minutes!
Here is the link
http://www.navigation.com/is-bin/INTERSHOP.enfinity/WFS/Navteq-HyundaiEMEA-Site