It's possible. I know the link to the BBTI link shows a slight decrease with the longer barrel. But, not with every ammo tested, and that is just 1 barrel. You never know what will happen when you are comparing different guns. It is common to see 50-100 fps difference, sometimes more, even with barrels of the same length. Some barrels just shoot faster than others.
I'd just zero both at 75 yards and call it good. Neither would be off enough between 50-100 yards to matter.