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Simple test for tracking is to see if the PV input voltage, assuming no shading differences, is the same for both arrays and CC's... The Classic's SOLAR tracking mode has been known to not be perfect for some arrays (rarely though, lately, AFAIK), but, changing to Legacy mode usually, at least, satisfies the question if it is or not.
Another sanity check is (usually) to at least swap the 2 arrays to the opposite controller and see what differences are observed. Then, sometimes, the measurments of the CC's can be off enough to show a loss or gain of one CC over another.
AND, if you are getting 90% of the nameplate of a particular CC, that would be considered pretty good. If indeed it is 90% of another CC under the same conditions and the same PV array, (just a different CC), then something needs to be looked at. The hardware efficiency just aren't that much different when up at high output currents/wattages to make THAT much difference in harvest (usually anyway)