Port and starboard bulkheads being damaged by water leaks

[JMB]

On both sides, the moisture seems to come near the junction of the cabin roof and the window frame structure, although I can find no evidence of water. The wood has been saturated to the point that I have repaired both sides, filing the area with a synthetic material.
Recently I have removed all overhead panels and have started removing anything that screws into or thru the cabin roof, such as the handrails.

Has anyone else had this problem and can help me identify where these leaks are coming from??

[S/V Deo Volente]

Are you talking about the back of the pilothouse? There are a number of joints in that area. I had leaks at most of the joints at one time. I had leaks around the windows themselves until I replaced and re-bedded them. As far as the fiberglass to aluminum frame joints I have used a hook knife to clean out the old caulking and then applied masking tape to both sides of the joint before forcing new caulking in place. I like boat life polysulfide.

[JMB]

While I have been constantly re-caulking in the way that Bob described, this winter and spring, I removed and re-bedded the seahood and took the inside overhead down to bare fiberglass.
I am concerned that my user error has prevented the posting of the various pictures I had added to Photobucket to show the various stages of my project.
Picture of the overhead before removal of panels.
  Picture of the panels removed showing the boards the panels screw into.
  Picture of the bare underside of the cabin roof.
  Picture of one of the 50+ bolts that hold the cabin roof to the aluminum frame.
  Picture of the overhead with the panels back in place and the repaired bulkhead.

I found many of the nuts loose so I added a ss lock washer to each and tightened them down.
By the end of May, I noticed no moisture or discoloration of the bulkheads.
I then cut and added a piece of teak veneer to make the interior look great.
While I never found any source of any leak, I have assumed that all of the steps taken solved the problem.
I then caulked every screw hole in the overhead before adding the boards and finally the panels and trim.