Since time is of the essence in many deals, that can be an issue. Also, while a VA is I believe 0% down, there is an up front VA fee you are responsible to contribute to, whereas conventional you are not.
I don't know all of the ins and outs of the deal, but maybe as around to another lender to see why -- or better yet -- have your LO better explain it to you.
Have your lender lay out the two programs side by side so you can see the comparison and decide which one you want to do. If your lender cant do this for you then find another lender!