What sort of sealant are you using? I recently rebedded and resealed the fixed (frameless) portlights on my boat (Sabre 34) and the factory recommended I use GE Silpruf.
You can get it in white or black. My portlights are "held" in by some screws that don''t penetrate the lexan, but rather hold the edges and let the sealant do the work. It works fine, but if your portlights are under some sort of bending stress, your job is much tougher. My last boat was a C&C with frameless, long portlights that were bent to conform to the cabintop. Leaks a''plenty. My current reseal job is working well.
Keep after it