I doubt it's an upper trap imbalance. Sounds more like your upper traps/levator scapulae are getting strained because they are trying to pick up the slack for weak scapular stabilizer when they are already under load trying to rotate and elevate the scaupla upward. This is just a guess though; it's difficult enough to assess this thing in person, let alone over the Internet.
You should search around for information concerning lower trapezius activation and start doing some scapular stabilizer prehabilitation type training. You may also consider doing a little bit of static stretching of your upper traps/levator scapulae prior to, and maybe in between, sets of overhead presses.
This is a start for you anyway. If it continues to be an issue, you may consider seeking out someone who can provide soft tissue services. If you still aren't seeing any improvement, then seek out a good sports medicine professional.



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