I have the same black digital thermometer/hygrometer that you do, and like you the humidity reads 99% in the egg box. My eggs are due to hatch in about 3 weeks and only show some minimal dimpling now.

Where is the humidity sensor, on top of the egg crate, on the eggs, up high...? Mine is up high. If you had it down on the egg crate maybe it gave a false-high reading from being too close to the substrate?