Which mods are you using? Do you hear the weird audio after moving an army on the map? I had a similar issue with my Planetside mod that was caused by some audio files that weren't being properly read by the game, even though they were the correct 16bit signed PCM encoding that the game requires. The strange thing is that just by having these sounds in there, unrelated audio effects in the game would be messed up.

To this day, I still have no idea why these files caused such problems. It may have been because there was human speech in them saying "We've captured the facility." and that didn't work well in the game for some reason. After removing them for the mod entirely (getting rid of the files, and any references to them in the .c5m) no further audio issues were encountered or reported. That is assuming you aren't using my mod, though.

It started when I subscribed to the Pirate Cove recruitment mod. But I had a bunch of mods already. Weirdly, it starts on the main menu, and persists in game with mods disabled from the in-game menu.

My Pirate Cove mod?
Well, at least I can say, that I never touched anything audio related in that mod in the way Baronfuming described above, no new audio files or anything.