There are at least three things that might affect your shifting.
The front derailleur has to be the right height. So if you put in a more compact crank, then the front derailleur has to slide down too.
The curve on the front derailleur has to be close to chord on the big crank. My first mountain bike had a Deore 26/36/46 crank (with Biopace too). When the 22/32/42 compact cranks came out, I made the conversion. The extra 4 teeth on the granny were important to me, and I wanted to get away from the Biopace eliptical chain rings. The new crank did not shift all that well I until I replaced the the front derailleur with the one that matched the crank.
The front shifter in a barcon shifter is not indexed. That infinite variability can accommodate a lot of situations that would be problems with other shifters. The front derailleur still has to be the right height.