I have disabled the stock [gallery] bbcode that comes with XenGallery in order to prevent the camera icon in the editor. The problem is that everytime I upgrade XenGallery the [bbcode] gets re-enabled again. And IIRC even if you delete the [gallery] bbcode, after you upgrade it gets back!
This is sort of as designed and not related to XFMG. The BB code definition is "owned" by the add-on updating the add-on that owns it will restore the settings. You'll see this in various other content types as well, such as cron entries.
That said, it might be reasonable to maintain the active status across upgrades. We do this in a couple places. That's likely the only change that will happen here though.