Most agents aren't interested in seeing a query again unless they give some indications to that, or so I'd think. However, I do have a friend who got the infamous 'form rejection', then resubmitted to an agency about six months later, and got asked for the manuscript. I know he updated the manuscript and reworked the query, so either that did it, or then again, there's so many queries flooding an agent, you might think that at times they forget you ever queried at all.
Also, some agents use readers to screen queries. If that's the case, perhaps the person doing the screening had a different taste in literature.