When using the auto-scheduling feature in Advanced Roadmaps I've experienced two issues: 1) sprints that were green before auto-scheduling are made red. 2) When checking one project to auto-schedule other non-checked projects are changed as well.
Can you provide more details on the algorithm used in the auto-scheduler? Maybe that would help me understand better what's happening and why. I've confirmed our estimates, our team size is what it is so I can't change that, and I've checked the prioritization of the issues. Also any details on settings that could help?