I repair motors as a profession so test motors on a daily basis.
As stated, there are a number of factors which can influence different readings between phases. We know for a fact that our workshop 230v supply is taken from what we call our 'blue' phase while the office supply is spread across the other 2 phases. The office supply across both of these phases is balanced and much less than the workshop load so we always get one phase, (blue), with a different reading.
Are your readings only marginally different, i.e. 1 or 2 amps?
Have you taken readings of the same motor at different times of the day and if so do the readings differ or remain the same? If they differ this could be due to differing loads at various times of the day.
What I would suggest is to take a reading of 2 or 3 motors at say 10.00am and note them down.
Motor 'x',
Time - 10.00am
Red Phase - xx Amps
Yellow Phase - yy Amps
Blue Phase - zz Amps
Do the same for motor 'y' and the same for motor 'z'
Then run the tests again at lunch time when the canteen will be in full flow with kettles/toasters/microwaves etc running and note down the results as above.
Finally run the tests again at mid afternoon but not during a time when people are likely to be having a tea break.
Compare your readings and note any differences in them. If they fluctuate at these times but still have a marginal difference then everything is probably ok.
Another test you can do if you are able to switch them off and isolate them is to move each phase cable along one, (i.e. Red is moved to the Yellow terminal, Yellow is moved to the Blue terminal and Blue is moved to the Red terminal). This will ensure the direction of rotation is maintained and by taking readings now and comparing them with your previous tests you will be able to distinguish if the lower reading follows the phase cable or stays on the same motor lead. If it stays on the motor lead it may simply be because of the way the stator is wound, (basket wound, rope wound, concentric wound, layer wound etc). So as you see there are a whole variety of reasons why they may be different but still be perfectly normal.
Finally, if you are still concerned you could always call in a motor repair company to do some 'on-site non destructive testing' procedures using specialist equipment which will tell you what state the windings are in and can give early indication of impending problems. from this you can then plan a maintenance schedule to have the motor removed and taken away for service/repair.
If you would like to know more you can PM me to save filling up the forum with something that nobody else would want to read.
Good luck and let us know how you get on.