I noticed that explosions were off, not always seeing the skull animation. Projectiles not hitting their target right at the center. Sound effects and music were having hiccups. I was using a modded, UFO Extended, XCOMUTIL-ed version.
Then I tried a clean install of v1.4, on top of it the data patch and latest GIT build, plus the three CAT sample files of v1.2. All of the above problems vanished. It is a totally different game now, very enjoyable!