This does not concern all the freezing issues since they acan also have something to see with loading time. However, make sure that your main PC is the party leader when you save your game and go to another module. All the freezing issues I had were due to the fact that I was using another NCP as party leader. Loks like a script is missing here.
For Other freezing issues try cleaning the cache by loading three other games and then try to load Kotor again.
There seem to be several problems with scripts setting/checking for global/local variables that fire when you enter a module. I did not directly verified the files yet but all the symptoms are there. At some places, I got the feeling that some of the scripts that set some plot globals are fired when you enter some modules and not when the action is perfomed.
Here are some examples of broken quests:
I was on Dantoine and saved my game just when entering a module and before talking to Vrook and fighting him. I died during the fight and reloaded my game. Vrook never reappeared, even when exiting and re-entering the module and it was really a big turning point in the plot.
Exact same thing happened on Nar Shadaa: I was suppose to meet "Visquis" ( in the "toxic" bar. I was playing as a Dark Side female sentinel. I saved my game just after I enterering in the area where you meet the Wookie if you are DS or Mira if you are LS. I met with the wookie. Until then, everything is fine. However, in the next sequence, I was transported to another module where Atton has to fight alone, he was ill equipeed and died. When I reloaded, the wookie never appeared. I got Mira instead and it was all messed up.
From what I have seen, this also happened to someone else with HK-50 on Peragus. After reloading the game, hk-50 would never attack you. I have also seen similar problems at other places but I don't remember them all but one involved a quest with t3-m4
Someone also mentionned a similar problem in the Tomb on Korriban when you enter the tomb with the "visions" and the door at the end would not open.
The above problems won't show up if you don't save/die at the wrong place at the wrong time...but when you happen to reload your game at one of those moments, it is really annoying as those affect major sequences in the main plot and you won't be able to finish the game.
How to deal with these problems
a. The solution I found is not to die or save before entering a module. Once you are in a module, you can also save safely after an event (examples: after the npc has spawned, after talking to the Wookie on Nar Shadaa but not before) but this rather annoying and not practical, especially for people who are not familiar with how plot advancement works .
b. Save often at different locations - I keep a rotation of 5 saves/planet and make sure they are not all in the same module.
- note: although I really hope Obsidian will fix this for the PC version, this issue will be fixable by modders - it is a matter of verifying some scripts and adding a few code lines here and there.