Sounds like you had a good tune to start with. I think the cells turn red when there has been a certain number of samples recorded for that cell and not necessarily significant changes in that cell. Sounds like the VE values are being fine tuned.
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2013 FLTRU, Jackpot 2/1/2 Stainless Ceramic Coated Head Pipes, Fuelmoto Stage 1 Intake, Power Vision, Jackpot Full Size Ceramic Crossover, MADSTAD 16" Windshield, Motolight Running Lights, Nostalgic Rails, Airhawk R, Hayden Primary Tensioner, V&H Roland Sands Slant Slip-Ons