Your CIMs may or may not be biased, but that's not the issue you need to chase first.
this line from your first post is what you need to address first
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When reading on the driver station the pwms to the jaguars show me that two are getting less than the other two.
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If you expect the wheels to all be getting the same speed command and they aren't you need to look at your code. I am not particularly familiar with the Labview holonomic drive VI and I don't have a copy of Labview this year to play around with so I'm not sure which direction to point you in terms of diagnosing the problem with the code.