Popping/Clicking Audio - I found out why

[artao]

I searched the forums and google, and found virtually nothing about this issue. All I found was a possible issue with Win 7 (and later?) regarding audio hardware acceleration. I cannot disable this on my system.
SO!
I downloaded SC Sound Edit and extracted all the audio files from every .agg in the game (one at a time, of course). Then I did a random sampling of these files.
LO!
From my random sampling, I can fairly deduce that the VAST majority of the sound files have the gorram click IN them.
Nice quality control there SCS :\
Well, the GOOD news is that Audacity (free open source audio editing software) has a Click Removal effect, which perfectly removes these clicks.
The bad news is two-fold:
a) there are THOUSANDS of files to process. however, they can be batch-processed in Audacity. ... this leads me to ...
b) some of the files are too short for the Click Removal to work. ... HOWEVER! From what I can see, most of the short files do NOT have the click in them

Do the rest of you experience this popping/clicking problem? I find it odd that I can't find it brought up anywhere really. It is quite annoying, frankly.

Anyone interested in joining together on this project to remove these annoying clicks? It's a bit overwhelming for me to take on all by myself -- mostly due to having to sort out the files that are too short for the click removal to work. very tedious.

Regardless, I'm sure everyone would appreciate a clean set of .agg files, eh?

NOTE: I did look in the RA mod as well, and the clicks/pops are in there too (at least for all the default platforms I checked. Didn't actually look at the added playables). LWAMI doesn't include any sound files, so fixing the vanilla ones would cover that as well.
EDIT: Yes, some of the other platforms in RA have the clicks in the audio files too. But not all of 'em. Odd

EDIT EDIT: and yes, i did do a full un-/re-install of the game to make sure my modded version wasn't all janked. it was in the fresh install that I checked the .agg files.