Silicon is a fine yet in my experience less permanent of a fix. What I have found that works GREAT is gutter sealant. Many of them are paintable when you get done if needed.
Another more pemanant option (although I never got there since the gutter sealant is working great) is using Vulkem 116. It is also paintable and from using it on numerous other projects can attest to its longevity and quality.
Let us all know what you decide and how it worked out for you.
Since I'm seriously considering yanking all the windows out and replacing with conventional RV type windows, I've decided to just remove the old sealant and caulk everything up to get me over the hump. For a long term solution the Gutter Sealant sounds like a good choice.
1985 International 28 Passenger
6.9L Diesel/Allison AT-545
What do you do about windows that you still want to use? My bus is a 49, I want to use most all of the widows but I am a little worried about how they will hold up in the rain. Although there does not seem to be any weather damage to the woodwork around them now. She has sat for six years. I have only had her for a week or two. But have found myself puzzled when it comes to the windows.