I have a 2014 with Entune/Nav so it may not be 100% relevant, but one annoying thing I've discovered is that my iphone won't sync via bluetooth when you have it connected to the 4Runner's USB port to charge.
On a side note, I unfortunately broke my iPhone 6+ last week, and upon switching back to my Galaxy S3, all of a sudden the options to even add new bluetooth device were grayed out on the touchscreen. Upon talking to the dealer, there was a new software update that came out somewhat recently that should fix it, so maybe your problem is due to a software update as well.