Postby Psy » July 4th, 2008 3:09 am
I can't answer this with 100% confidence, but a lot of times "komeru" is used in the sense of "with," like 感謝の気持ちを込めて kansha no kimochi wo komete "with a feeling of gratitude." If I extrapolate on that meaning a bit, with "negai" it becomes "with a wish" or "wishing that." If I'm not much mistaken, the phrase 流れ星に願いを込める nagereboshi ni negai wo komeru means "to wish upon a shooting star." Since komeru is transitive, you won't see it with ga unless it is changed to komerareru.
Wish I could be of more assistance, but I hope this provides a nice clue into what you're asking about.
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