For anyone who visits this issue in the future…
One solution to try is filling the DDC cache up using the command-line
< path to >\Engine\Binaries\Win64\UE4Editor.exe < path to >\ProjectName -run=DerivedDataCache -fill
I noticed one of the plugins was throwing an exception during this process. After disabling and re-running, the cache successfully filled up and the project stopped recompiling shaders on startup.