Sorry for the double post but I tested this and have steps to repro this.
- Load a track (doesn't matter deck 1 or 2) . not actually needed but it is for you to hear (stop hearing) as the sb2 resets and music then resumes where it was.
- Start playing it (again, just to notice the reset as the music pauses and resumes)
Press shift+(hot cue| autoloop | manual loop | sampler) - any combo will do. The light start sequence shows up (and if music loaded it pauses)
You can even load the song on deck one and use the combos on deck 2 and ddj-sb2 will still reset. Or vice-versa.
After this you can use the combo at will.
As a work around, just do it as soon as rekordbox loads and before start mixing so you don't worry about it for the time being.