Have any pictures of the grow beds as you are currently running them? You really want the seeds to stick to the damp layer above the flood level for the water. Some will usually get washed away but it sounds like most of them are for you. Try raising the water level to wet the media higher up and then lower it and seed right after this. More of the seeds should stay above the water level but you might have to mist at first if they get too dry.
If you're using expanded clay the media may be floating and for this you'd need to lower the water level (The media usually stops floating after a while). You may not realize this is going on, whole plants just disappear beneath the media or move around very slowly, all very mysterious
. This would probably deposit your seeds into the water and move them toward the siphon so it could be what's going on.You could also remove the siphon and Run Constant Flood for a bit while the seeds get established.
