It seems to be working for me in 1.4.1. No real game-breaking glitches so far as I can tell. I also have this issue:
Sometimes things don't fit quite right, or are just buggy when matched together. Solution is just to reposition or choose a different part configuration. It doesn't always happen for me even with identical combinations. Oh well! I just RPG it in my head and attribute the problem to budget cuts in my Kerbal Space Program (lol).