Hmm, I have 6. 1 and on the design page I can cause the class to flip by changing engines.
Are you using engines of the same size as your commercial ones? I've just verified in 6.1 that a size 50, x1 power, so military engine, does not cause the ship to become military. If I recall correctly from when the bug was tracked down, this is because the class design was still just looking at the engine size to determine if it should flip to being military rather than checking the engine power mod as well.