Just to reiterate because I think this is an important thread...

Advance upgrades won't clear on JFK-LAX except for extremely rare circumstances like an equip swap to a 767. You have to wait for the gate upgrade list.

This all hinges on your SWU being properly coded, which as mentioned would mean you have an UP2B priority on the airport list. If you have UP3 then you are being sorted by your normal plat status and not getting higher because of the SWU. You should be able to tell if you are #1 or close to that on the list. Be sure to call/ask agents what your upgrade priority is and if it isn't UP2B then get it fixed. The GA will likely not know how to fix it or that an SWU should give you higher priority.

You don't have to remove yourself from the comp upgrade... that has no impact provided that the SWU is coded properly.