...Well. I don't know what to call this. Oh well.
I do have a video of this, it's really low quality though. I'll try to get a better one.
This is kind of hard to describe, I'm not good with words. Basically what happened was, when soaring in the evening, the normal day theme plays. Then, if you get in a battle (through those birds flying about), upon leaving the battle, the night theme plays. I thought this was just a transition of time thing, but when I landed and used the eon flute again, the day theme was playing. Got in a battle. Same result.
I guess it's not really a glitch, kinda, but it's just something kinda funny I found.