There's an Enterprise Car Rental a mile or two from VPS airport in Valparaiso right on Government Ave (go right when you exit the airport and it's only like a mile or two down the road) and another one in the Uptown Station shopping center in Ft. Walton Beach right on Eglin Parkway. I've used both locations with no problems.
If they don't have a shuttle, it's a pretty short cab ride to either location.
And I agree to keep checking, and also see if you can get any sort of discount (AAA, occupational, those flyers that come with a credit card bill that usually go right into the trash) The last time we suddenly needed a minivan for a day, mister mouse found a discount code from the credit card bill thing, and Hertz ended up being the best price for things.