Sorry for the late reply but here is a little trick we use. The valves will be fine, however the wire connections over time will most likely corrode. A little trick we use while covering the trenches is to put a small piece of gorilla tape/duct tape over the hole in the valve cover to stop dirt from falling in. Since you say the boxes are not in low spots they are most likely filling due to water running over the valve cover.
You can also find valve covers without holes.
www.SmartEarthSprinklers.com
Cheers!