@chochajin I know practically nothing about this topic but it sounds somewhat similar to a problem I had with Microsoft IME awhile back. I had downloaded some new IME dictionaries that were used for all sorts of かおもじ and included preset phrases with some of them.
I noticed a few days later though that for some reason, whenever I would type anything using kana or kanji, it would give me complete gibberish. I couldn't even convert わたし to 私 correctly. Everything was just a one big mess. In the end, I ended up deleting the dictionaries I had DL'ed, and my IME went back to normal. I'm not sure if the IME just got confused with what dictionary was being referenced or what, but I tried selecting certain dictionaries to use and all sorts of other stuff, but it didn't fix the problem.
Like I said, my experience with IME is very beginner/limited. Just throwing in my experience because it sounded somewhat similar :/
Edit: I never switch between JP and English input either. No point as Jarvik7 said because JP allows romaji input anyway. Mine's set to romaji input default, and I have it worked so ctrl + caps lock switches to hiragana, alt + caps lock takes me to katakana, and alt + ~ switches me back to romaji.
I don't mess around with IME because I honestly don't understand the program much, but I do think that Windows can let you set whatever default you want, as another poster said.
2nd edit: I looked around on my IME. There's a lot of stuff you can change if you go to the properties menu. I think Tobberoth was right about not being able to set hiragana as the default input. Mine says hiragana is the default input method, but it doesn't work for some reason.
I think it only works if you set your keyboard to kana direct input instead of romaji direct input. Which is useless for me since I don't have a JP keyboard and I'll never remember which keys correspond to which kana
Edited: 2010-02-27, 8:47 pm