Damn, I think I downloaded an outdated version of this yesterday. I used Arch's installer (very nice by the way) and I had the humming problem.
I know I should try it on the newer version, but I have some information for the moment.
Windows Vista (32 bit), 1.6 GHz Intel processor, no idea how to find sound card info, I played as Dark Magic (just added it to the Megapack, so yea). The humming only happened in the tileset and soundtrack, not in the unit sounds. Also, the sound sounded like a telephone at the frequency that the tone started at. The tone usually lasted less than 5 seconds, but was still really annoying. Also, in the soundtrack I know this, the music wavered on one tone and then skipped to where it would have been without the wavering.