After messing around with it some more, for whatever reason, it appears that the game doesn't update the LS/DS Values until you actually gain some in game. Even though I had my DS value at 10, it wouldn't give me the option to acquire the prestige class. But as soon as I gained DS points through actions (killing Taran in the Dantooine port), the option became immediately available.
It also seems the bonus you get when you max out your LS/DS doesn't take effect until you do the same thing, or rather it doesn't even show up until you get some points.
Originally Posted by Hassat Hunter
Not sure how KOTOR decides your alignment. I once tried like you to alter the prestige gaining by changing 0 to 100 in KSE, however still only Sith options appear. Obviously the same is true for you (alingment change not accepted by the game in general, no prestige option).
Also, as mentioned before, there is a decompiled version of that file in 003EBO.mod.
Which means you probably would have been able to actually switch if you would've did something to gain LS points. Weird, huh?