Yes, all other holologs and cut scenes work properly. I'm going to try doing a clean game install and only install TSLRCM and M4-78EP, and see if I can reproduce the problem. I'll post back the results.
<Edit> Well, after a full day of testing, I've discovered that my problem was caused by VP's Peragus Tweak mod. As it turns out, I had forgotten to uninstall it after a previous playthrough, and it was still active. I uninstalled every mod and then reinstalled the game and TSLRCM 1.8.2 and M4-78 EP and then spent all day yesterday playtesting the game with just those mods, and then adding another mod, and restarting the game over. The problem only happened when I installed The Peragus Tweak mod, so that's what was causing the problem. Which really sucks, since I love that mod. </Edit>