Honestly? A VA loan, while it is a good product, is largely viewed as a "Snail" in relative terms. For one, a conventional or FHA approval can easily be done in 30-40 days. There is about 0% chance of that happening with a VA. Two, on the VA appraisal, they place the order with VA, and it's not uncommon for it to be 2-3 weeks before they go to the home and then another 2-3 weeks to turn the appraisal in, as compared to 2-3 days for the other.
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.