It has been a long time since I've used SolidWorks. I joined the as part of the campaign to get my company to go to solids. That being said, here is what my fuzzy memory tells me:
1) Sometimes models with multiple configurattions need to be regenerated a second time. Once to establish the geometry, once to establish the location. I'm sure that you've hit regen several times as you contemplated this.
2) Does either one of the faces in the model or one of the faces to which you are assembling disappear in one of the configuraations?
3) If one of the models in the assembly to which you are assembling (ugh--- that sounds awful) is underdefined, then any new model that gets assembled to it will also be underdefined. Look higher up in the model tree.
These seem obvious, but maybe I'll ring a bell here.
Good luck