Howdy! I'm not positive whether this will fix your issue or not, but there's another option you can check called "Playback starts at memory cue nearest beginning of track". You can find it in the DECK tab of your CONTROLLER section of preferences in Rekordbox. Give that a shot. It basically says "when you load a track, start at the first cue point".
I was confused by the same thing because for SOME tracks it would already land on the first beat automatically, while others would revert to that silent section even though I set the first cue point to the actual 1.1 hit.
So in other words, even though you set cue points, Rekordbox will NOT automatically jump to the first cue point you've set unless you check that option.

