Some time ago someone posted pics of the CPU innards, and there were two PIC24-series processors in there.
As for what was changed in the version 2 CPU, something in the way the external LED is driven. It could be as simple as moving the LED to a set of CPU I/O pins that have hardware PWM capability. Or, maybe a transistor was added to the LED common pin to allow PWMing all three colors by using a single I/O.
There could be other changes to account for parts availability, etc. Often there are board revisions because a part becomes unavailable and something else has to be used instead, or a cheaper part replacing a costlier one, or the same part is only available or cheaper in a different package type, etc, but with no affect on the actual operation of the unit.
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