MP3's are not a viable format for loops because of exactly what you mention. You cannot guarantee a loop will start right at the first sample and end on the last. You would probably run into this problem with any program that converts WAV's to MP3's.
No, you'll never be able to create perfect MP3 loops either. The nature of the encoding process forces a certain amount of delay to the beginning of the track. That's a limitation of MP3 that typically isn't a problem for long source material (songs). You could also try Ogg Vorbis. Ogg is a superior compression with fewer noticeable artifacts, it has better spectrograph analysis (I can show you examples), and it's an open format. AND, you can make seamless loops with it.
Sound Forge also supports .Ogg compression, and most major media players support it as well. Check it out!
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