Correctly sized chain with impossible too loose B-screw adjustment?
According to Shimano, the RD-6800 GS is designed for 28-32T largest cog, where the SS is designed for 23-28. 
http://bike.shimano.com/content/sac-bike/en/home/components11/road/ultegra1/rd-6800-gs.html
http://bike.shimano.com/content/sac-bike/en/home/components11/road/ultegra1/rd-6800-ss.html
They may have actually done something different to the body of the derailleur instead of just putting a longer cage on it. I don't know that for sure though.
Of course, that doesn't mean the GS can't work with 25. 
Your chain length shouldn't affect the B position at all. It will only affect the rotation of the cage around the upper pulley.