There was a known issue in 4.1 that was quite similar to what you are describing.
it should have been fixed in 4.1.1 though, so its probably not exactly the same thing.
It shouldn’t acctualy have to compile the shader unless you specify it to recompile out of date ones
I haven’t yet found an option to automaticaly recompile out of date shaders, and for as far as I’ve understood, you need to mod the engine to acctualy allow for full recompilations of the shader library.