My formerly leaky windows sound similar to yours except the rebates are in the outside of the cabin and the windows are held in by S/S frames and lots of screws. I was advised to use Marineflex Bedding Compound available here. It's a non-setting polyurethane which means it sticks and stays stuck, you just have to be careful to clean all the exposed sealant away once the joint is made. I rebedded my windows a month ago and so far so pleased, it seems to be a lot more waterproof than the previous arrangement which I think was some sort of silicone rubber.