This was really weird, but the problem was solved just by restarting my computer. Closing and restarting SCIM alone wouldn't do the trick. Here's what happened in case someone else has a similar problem.

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I'm running SCIM 1.4.6 on Debian Squeeze. I am able to switch among a few input methods like English/Keyboard, English/European, 智能拼音, Stroke5, etc. However, I cannot select Raw Code, nor my own user table which I made for Spanish characters (accents, etc.). They are both installed, they both show up on the tables list and on the list of installed input method services at the Global Setup. However, neither of them appears on the selectable input methods list.

Moreover, I have disabled some of the input methods, and yet I can still select them. I have tried restarting SCIM several times, uninstalling and reinstalling those input methods, and nothing changes.
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As I said above, restarting my computer solved the problem. >_>