I have 2 rifles:

Complete Bushmaster with 14.5" 1/9 flat top with Eotech 551 and a Bushmaster lower with a Colt 16" 1/9 HBAR flat top upper with Eotech 511.  Both rifles are zeroed at 25 yards and POA is POI with 55 grain FMJ.

At 50 yards the 16" keeps the POA / POI, but the 14.5" shoots about 2 inches high.  Is this because of the 1.5" barrel difference?

Quoted: I have 2 rifles: Complete Bushmaster with 14.5" 1/9 flat top with Eotech 551 and a Bushmaster lower with a Colt 16" 1/9 HBAR flat top upper with Eotech 511.  Both rifles are zeroed at 25 yards and POA is POI with 55 grain FMJ. At 50 yards the 16" keeps the POA / POI, but the 14.5" shoots about 2 inches high.  Is this because of the 1.5" barrel difference?

Most likely. I have an Olympic 16 in, zeroed at 100 meters, and i am 2 inches low at 25m, 1inch low at 50 meters

Quoted: I have 2 rifles: Complete Bushmaster with 14.5" 1/9 flat top with Eotech 551 and a Bushmaster lower with a Colt 16" 1/9 HBAR flat top upper with Eotech 511.  Both rifles are zeroed at 25 yards and POA is POI with 55 grain FMJ. At 50 yards the 16" keeps the POA / POI, but the 14.5" shoots about 2 inches high.  Is this because of the 1.5" barrel difference?

Congratulations!  You have defied the laws of nature and contradicted priciples of physics held to be true for hundreds of years!

IF (and I emphasize IF) both rifles are POA/POI at 25 yards, then both rifles will hit exactly the same amount (for all practical purposes - tenths of an inch don't count) high at 50 yards.  If this is not the case, then the rifles are not truly zeroed at 25 yards.

BTW, I would recommend zeroing at 50 yards.