It works like a charm but it's a bit of a strange way of changing the colors.
After reading through and testing, here are all the steps in order for this error to be fixed guaranteed.
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Set the controller's colors to whatever you'd like. Then press "Write Colors"
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Go to More...>Debug
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Change the "Subcmd arguments:" to "1B6000000102"
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Change the "Subcmd:" to "11"
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Click on HD Rumble Player
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Go to More...>Debug
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Press Send. Your Pro Controller will now be properly colored!
Originally posted by @dankonion in #28