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When I go to play the song in TF2, it sounds somewhat choppy and irritating to the ears.

Everything is in the correct structure, I am 100% sure. This happens to a majority of my songs and even happens when I create my own private server or join a pub.

I have one song (Organ Donor) that plays nicely and the other "Smells like teen spirit" which plays choppy. They are the same format, frequency, bit rate, etc.

Ideas?

Thanks.

If both songs differ in under the same conditions and scenerio, it's definately a conversion problem. Have you also tried the sample wavs (see the sticky in this forum)? Try reconverting both songs from original source using exactly the same converter (say Audacity) and conversion process.
Other than that, another thing to note is that some songs given their nature may sound a bit more fuzzy or distorted, check out Reducing Bass & Volume for tips on this.