I looked in to this issue months ago as I noticed this problem immediately "after" buying the truck on my first conference call on the way home from the dealership.... After digging in to it seems there's commonality for the users affected.... IPhone's connecting through CarPlay and those phones have the Waze app installed. Waze as long as it's installed on your phone has partial control of your microphone and it seems that Waze/Carplay and Sync fight for control of the microphone. Remove any one of those variables from the equation and things work. For example, deleting Waze from your phone and trying again should allow good calls with Carplay/Sync. Alternatively, keeping Waze but disconnecting Carplay and just using Sync Bluetooth also works (which is basically what I do to take calls in the truck). It's annoying but Sync isn't really the only problem here, it's also a known Waze bug....
If you google "Waze Microphone issue w/ Sync" you'll find all sorts of hits describing the issue with unfortunately no fix that I've seen yet.