Hmm. We didn't really see grown-up Windkin until Tyldak and Kahvi tried to steal the Little Palace. I wonder if meeting his birth father had a negative effect on him? "I have tried to think well of you, until now," Windkin says-- or words to that effect. It must have seemed to Windkin that his birth father went from being Winnowill's minion to being Kahvi's, doing whatever either of them said without question as to right or wrong. That, and watching the bloodshed later between Go-Backs, Sun Folk and Wolfriders over the Little Palace, may be what soured him. And the encounter with Door just confirmed his reasons for mistrust-on-sight.
I agree that the reason Windkin gives for mistrusting Wavecatcher-- that any shapechanger reminds him of Winnowill-- didn't quite ring true for me. After all, Windkin never encountered Winnowill again after infancy.