"if I was not checked in orginally, went back 'un-requested' the eupgrade and then re-requested....should it have gone through then? "

No -- you still have to do it manually (i.e. request on line or through an agent once you are unwaitlisted--being checked in makes it difficult; being checked in with luggage already going makes it impossible). What happened to you is the common (but dumb) way AC implements this. Hopefully our friends at AC will solve this.