RPG maker has a trouble on reading the mp3 files (specially the longest ones) when looping. And probably wav too. Use an absolutely custom audio system to fix only this is a doom. Also, I don't know about any costum audio system which could fix this bug completly and efficiently. The good thing is, usually ogg is well readed. So you can convert your mp3/wav files to ogg and try it back.
Edit: Oh sorry, maybe I misunderstood the initial problem, if it's a blank space on the start/end of the song try what Blizzard said. Also, Audacity could fix the problem. And if it's a loop "jump" problem in all the songs, in my particular case what works better is to change the mp3 format. I'm not saying it's the only way.