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If you still have the old code around you might try monitoring delta_t to see if it is greater than 0 while the auto code is executing. It would be easiest to simply save the greatest value delta_t reaches during loops and then either use the OI user_display_mode or a debug statement outside the auto loop after the auto finishes (so the debug slowdown isn't an issue) to display the high value.
From your description of the symptoms it sounds like the separate slot definitely had an additional delay for some reason and the new implementation doesn't have that delay.
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"Rationality is our distinguishing characteristic - it's what sets us apart from the beasts." - Aristotle
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