I have a leaky skylight, I actually think that the leaks are coming from the seal between the glass and the frame rather than around the flashing or anything like that. What is the best calking / sealant to use, obviously it has to be something that is UV / Weather resistant, preferably clear, able to flex in hot and cold. Any suggestions?
Just don't use silicone sealant as you cannot paint it, leaving the window doomed to future failure.
I use paintable caulks which are advertised for use in marine type environments (read boats etc.), on the principle that if it's good enough for a boat, then it should be great for a window etc. as they face a similar weather lashing.
It's pointless mentioning brands as they vary country to country but just make sure what you choose is paintable and very expensive! Cheap stuff usually has hopeless durability, whereas the big brands make stuff which lasts decades.
Most of my customers are regulars and I'm old enough to see some of the work I did 25 years ago plus, and some of those old sealants are still going strong.
Incidentally, what is the original sealing system used frame-to-glass? (rubber seal, putty strip, etc.).