The previous behavior was sort of accidental; the tags were ordered by the Id of the row used to store them, and since those rows were usually deleted and re-created, those Ids tended to just increase as you manipulated the list.
But not anymore. In preparation for some coming enhancements, it's now possible to modify these rows in place - and as a result, they aren't necessarily deleted when you remove the tag from a list (or move it between lists).
As a work-around for the folks who relied on the old behavior, I threw together a userscript: Reorderable Favorite Tags.
This'll restore the previous behavior: tags will remain in the order in which you add them, and also allow you to reorder the tags at will by dragging them around (you have to start editing them first though, so as to avoid inadvertently reordering them while trying to click).
Try it & let me know what you think. If it works for you, I'll throw it up on Stack Apps for others to use / enhance.