Chronic window leaking

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Neither is caulk. IF you only want to seal it temporarily JUST to stop immediate leakage I would use a cheap Home Despot latex caulk. Temporary ONLY! Easy to apply, cheap and not difficult to remove. Save your $$ for the proper materials when you do a proper repair. My $.02.
Is this the one you mean?
Dap acrylic latex caulk

There is a similar caulk that has silicone. The above link did not mention silicone.
 
Is this freezing cracks of the gelcoat?
The connection between flybridge and the cabin roof is hidden inside, how to check it?

View attachment 155987
Yes These are typical freeze cracks. The moisture inside freezes and an expands and caused this type of crack. It is a bit away from the window . Most flybridges have external flanges that are screwed down. The screws over time weep into the structure and run down. I suspect you have exposed screws somewhere above. Maybe behind that trim board with the screen.
 
The best procedure would be to remove the window completely and clean off any old caulk, then rebed. Trying to caluk without removing the window if it does work will be a short term fix since the window will work with the wave action and heating and cooling. Then the caulk applied on the outside will give way.
I read through the entire thread and agree with Dave. You need to remove and re-bed the window and if necessary replace any rotten structure underneath. I re-bedded all 7 windows in my pilothouse. It was a day per window, once I got the hang of it. Some were leaking and some were not. None leak now. The work was done 9 years ago now. Also re-bedded two windows in the saloon, including replacing a broken slider window pane and re-bedding the fixed pane as well. Trying to just apply caulking without removing the window is not a long term solution.

Jim
 
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