All I can say is that this is a particularly annoying problem that will never officially be fixed....ever....bad port??...perhaps...but anyway its either crackling sound or too low sound....or both which was my problem...and drove me nuts for a good few hours...
This kind of works....kind of as in it can depend on your system...however it doesn't matter which version you have...can be retail dvd or steam...doesn't matter...
1. Download and unzip this:
Mirror 1: http://www.megaupload.com/?d=1MGHUHVD
Mirror 2: http://www.4shared.com/file/jFvgM5Bv/scarexplorer10.html
2. Run the program and go look for 00audio.rcf (in the prototype install folder)...click Extract and then All Files....choose to extract everything to your desktop.
3. Do the same for 01audio.rcf 01woi.rcf 02woi.rcf 03woi.rcf and 00woi.rcf...this will take some time.
4. You should now have 2 folders on your desktop...Audio and Movies...Open the audio folder and cut everything in there.
5. Now open the Prototype install folder and paste everything into the Audio folder....if it asks you to overwrite click "yes".
6. Cut the movies folder on your desktop and paste it into your Prototype install folder.
7. Rename all the files you extracted (00audio.rcf 01audio.rcf 01woi.rcf 02woi.rcf 03woi.rcf and 00woi.rcf) so they are called something different...even if its just adding a letter somewhere.
8. Go into the audio folder and delete the ambience.p3d.
Try your game...if the problem is solved then stop now...if it isn't continue.
9. Download this replacement dll...it normalises the sound levels in the game...but for me also removed the crackling permenently:
Mirror 1: http://www.megaupload.com/?d=0HGOPJLM
Mirror 2: http://www.4shared.com/file/GNkd7lR6/prototypeenginef.html
10. Go into the Prototype install folder and rename prototypeenginef.dll...just so you have a backup...then copy the fixed prototypeenginef.dll in the zip into the folder.
That fixed my problems.