I have almost the same issue, but I think it's related to app updates. The setting that always gets lost after an update is my starting location (set to a favorite). The favorite itself does not disappear, but the mapping to startup location is lost. BTW I don't have GPS enabled. I always want Windy to start at my home town, not my current location.
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RE: settings not saved
Map center moves when pinch zooming
When trying to zoom in, the center of interest moves. Said another way, if the map is centered on point "X" then after zooming the map is centered on a different point. That new point seems to be where the first finger (of the 2-finger gesture) touches the screen. I have a Galaxy Note 10+ with latest updates to OS and Windy. Great app, by the way.