We've had excellent results with Dow Corning 795 silicone. A local boat builder/repair expert recommended it to bed our plexi windows, and it has been leak free since installation, with no separation developing.
A friend with windows similar to yours removed the old gasketing material altogether and filled the frame space with the above silicone, cut some spacers from the old gasket to locate the pane in the frame, the reinstalled the frames and has had no leaks since. Mask off the frame and the lens prior to re-assembling things
It's not easy to find, not usually in the Home Depot section, but look for a wholesaler or a HVAC/plumbing/insulator supplier.