IIRC from posts in the past, I believe the problem originated from how the game was originally ripped. When the game was ripped, an extra 2 seconds might have been added to each audio track if BINChunker was used to convert the BIN/CUE rip to an ISO/WAV or ISO/MP3 format. When you burn the ISO/WAV or ISO/MP3, you burner automatically adds 2 seconds of silence between tracks, thus causing the delay you're experiencing.
If you're up to it, you can try to cut 2 seconds out at the end of each WAV with an audio editor (e.g.,
Cool Edit) to cancel out the extra 2 seconds on each audio track. Afterwards, attempt another burn and see how it goes.
