I've encountered a bug where upon entering the Korriban Sith Academy the cutscene of my party members commenting on the place and Darth Sion getting up from meditating doesn't play. I'm quite sure it has something to do with either or both the the Dark Jedi Conversion mod and Sith Assassins with Lightsabers mods I have installed. Or is this just a common issue?

I have never experienced this in my K2 but have seen something quite similar. I am reworking the Endar Spire module so that you are part of the Sith boarding it. When I put everything into an ERF, which if I'm certain is what most modders do, it completely skips the scene where you wake up. The solution isn't written in stone but I think it has something to do with the scripts not being in the override folder or at least something to that effect, a file not in the right folder. Unfortunatly I can't tell you what file needs to be moved nor what to do. I hope this helps you to an extent!

Got it. It was one of the Dark Jedi Conversion script files. Removed them all to make sure, then added them back in after I got the cutscene because I want some Dark Jedi in my game. Hopefully everything goes well in Telos...

Hmm, that's interesting. I never had that issue when I made it (that was part of the game I used while testing). Glad you got around it though. :)