in those amounts the caramel isnt going to add much (if any) color.
mash duration shouldn't matter as with an efficient system you should have full conversion in 30 minutes. so changing from 90 to 60 shouldn't matter.
I'm curious your sampling of the color, 20-35 is a relatively noticeable difference but with any haze or turbidity you may have a difficult time differentiating the two (this is why professional samples are usually spun clear or checked on a haze/turbidity meter)
it seems that judging by your session data, this was a pretty awful attempt at the recipe. You show a 56% mash efficiency, so if the program is allowing for a 70% efficiency and you came in 15% lower, it would make sense that your color, as well as sugar, and everything else would be off. If any of this session data is accurate, id say you need to work on becoming more consistent, then tweaking the program for that consistency. at that point you may get more accurate predictions.