Fixed in next version 0.7: Pinned tabs remain pinned after changing container. However, due to API limitations, tabs have to be positioned back into their original order.

Why? This has to do with how the add-on actually changes a tab's container, which is, by duplicating the current tab into a different container tab and then removing the original—which is the only way to do this using the API, and pretty much an unintended usage; a hack, if you will.

Since the resulting container tab is pretty much just a new pinned tab, it will always be added to the right of the rest of the pinned tabs, and there's no way to control its position thru the API. Therefore, only the user can reorder pinned tabs.

Additionally: An add-on like Multifox had considerably more access to the browser than a WebExt add-on could ever have, and therefore not all features can be exactly 1:1. In any case, it has never been my intention to replace Multifox, but to allow exactly this one extended functionality to the official Container Tabs add-on/feature by Mozilla.