Have you deleted the pairing since upgrading? Have you made sure the headphone are connecting as music, rather than headset?
My Sony BT headphones are far better with WP8.1, with 8, they sometimes would only pair as a headset, so I needed to turn BT on/off till they connected correctly. They don't do it with WP8.1
Lets not forget, BT will involve interaction with firmware, so your problem may sort itself with the official 8.1 build.