Slightly dumb question, really, but it's the first thing I can think of - are you completely sure the files themselves don't have 2-second-silence gaps at their start?
That can happen if a cd is not ripped the right way for gapless recordings (i.e. disc-at-once rather than track-at-once). Obviously rockbox is only going to be able to avoid adding additional gaps, it's not going to skip over gaps that are already encoded into a track. (Maybe that's a bit too obvious a point, but aside from that I don't know what the cause of the issue you are having is - gapless seems to work fine for me on my 7th gen).
(If you do have the 2 second silence at the start of the tracks there are utilities that can strip them out)