Water water but where from?

If you look closely at this pic you can see what looks like a scupper in the ply wood and a scupper type of path in the fiberglass. Got to look into the paint.
 What is happening is when it rains we are getting water from this spot that drains to the very upper bilge then to the under engine bilge then to the lower bilge.. A lot, like a couple inches in the lower bilge.
We have looked all over the starboard side of the boat while it is raining and do not see where the water would be coming from.
At first we thought it was from the mast but now that the engine is out it is clear to us that this in not from the mast.
Debbie filled the water tanks and then painted the bilge. It took several hours to paint the bilge and then we hung out for a while and so foth. Not a drop of water in the bilge. So we are thinking it is not the water tank.
 We can let the boat sit for days and if there is no rain the bilge stays dry.
  We will test it out by re-filling the water tanks to max then with no rain let it sit for a few days.