KSE has been working fine for me. I've used it multiple times on multiple save files for every imaginable reason. I have the following currently installed:
1.0b patch
HQ movie patch
HQ Music patch
TSLRCM 1.7
Unofficial 1.7 Fix
Shem's Ultimate Sounds Mod
Realistic Nar Shaddaa Skybox by Sharen Thrawn
Goto's Window Fix by Darth Insidious
Cyan Lightsaber Fix by Marius Fett
Coruscant Jedi Temple by DeathDisco
Better Male Bodies by Trex
Movement animation fix
Any Spell Mod
Shem's Realistic Visual Effects
Sion's Arrival to Peragus Fix 2.0 by zbyl2
Telos Shuttle Crash Movie Fix
All of them linked on the OP or downloadable here (well, except for the official patches, anyway)