If you have had silicone used to seal the windows, then buy some silicone eater from Screwfix or Toolstation to completely remove all residue. Silicone leaves a layer that virtually nothing else will bond to.
I agree with Stemar to use butyl rubber to seal in the windows.
Another vote for Hadlow Marine. They did a cracking job refurbishing all of the windows on my Westerly Berwick 5 years ago. Very pleased with the result.