Joe:
100 mV is only 0.5% of 20 V, so even a few hundred mV isn't really a significant number. For motor voltage read to the nearest 0.1 V and take the (Max+min)/2.
For 3 Amps, we would expect voltages near 0.6 V. Again, voltages probably within the nearest 0.010 V will be fine (Max-Min)/2.
As for why things are not steady. A two phase motor. Right there there is an opportunity for jumpyness. We do care about both average currents an peak currents, but it's not something YOU can do. It either requires a scope (Preferably storage) or a peak-hold meter. Don;t worry too much about the actual numbers.
I did measurements once where 1e15 ohm-cm was basically the same number as 3 e15 ohm-cm, yet the second number is 3x larger than the first.
Being, Two phase, temperature, turbulance and Additude (A fancy word for orientation of the motor) , Stiction (Start up friction) will all play a part.
Now, we are interested in starting info. Your numbers "could" be better, say if you left all of the motors in the bucket for 24hrs or even an hour before starting the test. I can't be 100% certain though.
Don;t worry about a 5% do the best you can. 10% of 20 V is 2 V, 5% is 1 V, 2.5% is 0.5V. Now the readings don't look so bad, do they?