[...] the output seems to be really inconsistent when driving the wheels at a constant speed.
What is their resolution?
What wheel size do you use?
How did you mount the sensors?
Did you remember to add pull-up resistors to each of the 3 channels?
Did you put a cap over the supply terminals?
How do you read them?
How does the inconsistency manifests itself (in numbers)?
The encoders you have should work extremely well if handled correctly, but they don't accept as much positional tolerance as a home made sensor would.