Does the Lead have a Role in each Opp? That's the only way Marketo will be able to know which stage.
I am not 100% sure about how Marketo handles multiple opps on the same Lead. Perhaps RCA is able to manage this better.
Going out of the box a bit, I've used Segments to figure out the craziness of a person who has multiple Opptys. Basically, put all the logic and rules into the the segment and let that figure out which stage the person should be in. I've been using Segments more and more for driving RCA stages and it seems to be working (Although there are some gotchas since Segment changes aren't always recorded consistently or quicky)