I noticed the hole where the top silicone piece sits has to be completely free of water. One of mine kept overflowing from a bit of moisture causing it not to seal correctly.
At risk of offending, I will offer a correction - failure of the top seal cannot cause overflow. It can cause over watering, but not because the maximum water level increases. The over watering, if symptoms develop, happens because air leaks into the inner float chamber through the valve, causing the water level inside the float body to go down at the same rate it does on the outside of the float body. Normally, the water level inside the body stays high enough to keep the inner float valve securely closed
until air can get beneath the bottom edge of the body. This is why the Aquavalve forces the plants to use all the water/nute solution before re-flooding the tray. If the top valve leaks and allows air in, the water level will cycle from something like ~~1/2" or so deep and the normal maximum level. This means that the bottom 1/2" or so of the pot will be continuously flooded instead of periodically drained and aerated, which may, or may not, cause problems of overwatering, but is not how the Aquavalve is designed to operate.
The maximum height of water in the tray is controlled only by the inner float valve, and if overflow occurs, this valve is not operating properly, likely due to contamination of the seal area with crud, distortion or poor seating of the silicone, or physical damage of the hard plastic lip that the silicone seals against. Never use anything hard to try to clean the plastic seal surface or clear out the hole that liquid moves through. If the sharp lip of the seal surface is damaged, the entire valve is toast.
You are correct though that water beneath the silicone of the top valve could prevent proper seating of the silicone, and that could cause malfunction. Both float valves work properly only if the silcones are fully seated, seriously clean, and the silicone surface undistorted. It is a really good idea to have a supply of fresh silicones on hand, and if cleaning the Aquavalve and re-assembling does not fix mis-behaviour, the next cure is to replace the silicone(s) with fresh ones.
Good luck with your grows, and please don't take offense at my correction. The more discussion of how this unique little valve works here the better.