Well, I can only fix bugs that can I can reproduc, or otehrwise understand and that's not the case here. You should put the LSDj side in either slave or MIDI mode — MIDI is recommended because slave gives a one tick lag when used with this ROM but either mode will work — and then press start. This should put LSDj in "wait" mode unless there's something already sending a sync signal. It is recommended to first put LSDj in wait mode, and then start playback on the other side, so the two side start playing at the same time.
Are you able to sync two copies of LSDj?
That's exactly what I did, and I did even try midi mode just to see if it made any difference. I will mess with this further when I get home and report back. Would LSDJ version matter? I believe I'm using 4.6.2 iirc.