Update: Spoke to the owner at the dealership. They will take the unit in at the end of the season (i have a seasonal so i don't want to take it now and lose time). Turns out someone at the dealership put the caulk on and shouldn't have. They said they will go through the whole list, fix everything and make sure I leave happy. If they make good on that I am fine with it.
In regard to the leak from the vacuum breaker. This is pretty interesting. Upon further inspection I noticed that FR cable tied the vacuum breaker against the wall on the inside of one of the cabinets. They mounted it very high up in the cabinet about 1/4 inch from the shelf above it. When I turned on the the water, there is a small plunger inside the valve that rises and seals off the top. Well, mine didn't have enough clearance from the shelf above it to seal off fully, hence, the leak. I thought I'd call Swain Industries (company that makes San-T-Flush products) to ask if they made an alternate vacuum breaker valve that was designed better than the one they supplied on the flush system. After looking at some pictures we determined that the safety cap on top of the valve was missing. This cap covers the plunger/seal so it cant hit anything when it opens. Therefore, you are guaranteed perfect clearance regardless. They sent me the cap - problem solved.
I week later I get a letter from them saying that because of my call they did an audit at the FR factory in Oregon and it turned out that FR has been installing these breakers without the caps on any of them. This has been causing leaks in trailers everywhere. Anyway, at least Swain cares enough about customer service to take the initiative to investigate why it happened and has taken steps to resolve the installation issues at FR.
Sorry this post is so long, but i guess if you have a black tank flush on your FR from San-T-Flush it would be worth checking to see if your vacuum breaker valve is leaking due to the missing cover. The cover not only protects the seal clearance but it prevents debris and dust from getting in the top of the valve and affecting the seal. Swain also said it prevents the occasional squirt from coming out of the top too. This is normal and happens every so often if its uncovered.