There is no way to predict the cancelations- I have seen them throughout the day. If it is a MUST DO, then double book and be prepared to either go twice or eat some cancelation fees. A possibility would be to book with TEMSCO who flys to both Juneau and Skagway- they may offer more generous cancelation policies if you book both trips with them???
As for the experiences from each city- a glacier landing is excellent no matter which area you go out of.