I don't know if it's just me, but usually when I see a preview for a movie, I'll search out a bit more about it before I decide to go see it. Most times, if the ending or rest of the plot seems like a stretch or doesn't make sense, I won't go see the movie. I'm guessing most of us are the same. Why would I go see a movie that MIGHT not be good, when I can go see movie b. whose preview pulled me in completely and any other spoilers I've found about it seem awesome?
The preview is your query letter. Most queries are terrible. But yours sucked someone in--they wanted more. Now they had two choices...they could "see the movie" (read the mss.) or "read the spoilers" (synopsis). Agent chose to read the spoilers. If you REALLY feel your ending works and is completely justified, then perhaps the problem is in your synopsis. You need to show WHY this ending works in those few pages, and it's possible that's not being done in the best way possible.
