xProcess

Thanks. Your right that I managed to figure out most of for myself - right after I posted the question. I hope this may help other adopters. I think the main part that confused me was that since the project setup has a place to enter the overhead % I never considered looking at the overheads until almost by accident I did and realized what must be going on.

I'm sure I'll be posting back here, probably soon. Our team is not the typical Scrum case study, so we have some issues that most tools don't seem to cover and we're hoping that the flexibility built into xProcess will allow us to get something that better fits our needs.