This is interesting. I opened both files in Sound Forge. Setting both files to loop, there is an audible click in Jaques, but Harry loops smoothly. This is the opposite way round to the problem you describe. It is also clear from these particular examples that DC offset is not an issue, I seem to remember this maybe only affecting the vocal fx, but I can't really remember.
On closer inspection of Harry by zooming in to the waveform, it seems that the beginning and end points are very close to 0db, and it loops glitch free. I have tweaked it a little bit to make sure it exactly hits the zero crossover at each end. This may help?
But further inspection of Jaques shows that the beginning point does not start at 0db and also that at the end it does not quite finish a complete cycle, and therefor glitches when looped. I have fixed the issue here to make it loop correctly in Sound Forge, but it is interesting because you say this one was already fine within the game?
I wonder whether there is a glitch in the game's audio engine, and the workaround discovered by Stainless was to set loop points slightly early or late of zero crossovers?? To test this theory please could you send me another example of one of your loops that does work and and one which doesn't?
In any case, I have tweaked both files you sent me, and you can download them below. I would be interested to know whether it makes an improvement.
Ya very strange, Jaques is the fine one for me but Harry's is not. Here is another set here. EFIRE.WAV Clicks, ESTILLETO.WAV doesn't and sounds fine. Lol the news ones ya sent me are still doing what they did, man weird! Jaques is not clicking and Harry clicks like a son of a... I don't get it bah lol this funny oh yeah the link is below for the new ones. Me very very sad, very mooch :( Never thought I'd have this issue never did before on other game WAVS but they were newer games and used a bunch of formats but WAV was one of them. Might be a game issue but I shoudl ask ya, Stainless engine sounds (WAVs) click on my system they click on yours? I really don't get it even Carmageddon 2 does it. TDR, didn't seem to but meh piece of low quality junk audio anyway on that one, well possibly it does but I hate what they did with the audio on that one rather not fiddle with it, I'm going to ignore that one.