Which software version are you running? 1.03 and 2.0x use different playback engines. A file that plays fine on one engine might not work on the other and vice-versa.

Please save a copy of one of the "bad" files. If it will play in WinAmp, but won't play on the 2.0x software, please e-mail support and see if they want a copy of the file to analyze it.