Yo ejj,
How are you switching back and forth between the Red and Blue comp? If you're using just one FX slot (say FX 1, slot A) and using the model select knob to change between the pedals, then what you're seeing is expected behavior.
If you're wanting to A/B test two different models with your own custom settings, I would put the Red comp in (for example) FX 1 slot A, the Blue comp in FX 1 slot B, and then switch between them.
Someone correct me if I'm wrong, but I'm fairly certain that turning the model select knob is always going to give you factory settings for whatever model you change to. And if you've got autosave on, turning the model select knob effectively erases whatever custom settings you had before you turned the model select knob... because when you go back to select the original model you had in that slot, you're gonna be starting over with factory settings again.