Check EAC. If it is set to "Append Gaps to Previous Track" in the action menu, then the gaps could be from the original CD. For example, if there is a 2 second gap between songs 2 and 3 on a CD and you use EAC with the option above, then your encoded version of song 2 will have 2 seconds of silence at the end. If you then make a mix with that encoded song there will always be a 2 second gap after the song.