This 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](https://meta.stackexchange.com/questions/305560/2018-monthly-product-team-updates/310126#310126), 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](https://gist.github.com/Shog9/c13c28c33f466ba7195cb9fd0eafc93a/raw/reorderablefavoritetags.user.js). 

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).

![demo](https://i.sstatic.net/QAVKi.gif)

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.