You might find these MS DOS (= mpc compressor) windows annoying, but they are useful: if something goes wrong with compression, you'll see it.

What can go wrong? It is possible that the MS DOS windows immediately disappears after popping up, meaning that for some reason the MPC compressor could not compress the WAV files (usually a bad commandline). Resulting in a big (e.g.600MB) uncompressed album (WAVs instead of MPCs). But that is not too important: apart from an absolute beginner, anyone will see the album is too big (even if their EAC hided the MS DOS windows).

How to make EAC hide those windows?

'EAC' > 'EAC Options'

Choose the 'Tools' tab and check 'do not open the external compressor window'