Hi Jon,
You asked for SuperSorter's automatic sorting to be suppressed when you are working in the Bookmark Manager. I have added this feature in version 0.5.3, which should come out within the next few days.
If the Bookmark Manager tab is active (that is, if it's in the foreground) then neither the manual nor the automatic sort will start. This is a configurable setting that can be turned off via the Options page. Note that it only prevents a sort from starting if the Bookmark Manager is open; if you open the Bookmark Manager while a sort is already underway, SuperSorter will continue and complete that sort, and items will still move around inside the Bookmark Manager.
Incidentally, the slightly odd behaviour you noted happens because when other tools make a change to Chrome's bookmark tree, the Bookmark
Manager takes a bit of time to catch up with the changes. So SuperSorter can finish sorting and you may not see the results in the Bookmark Manager until a few moments later. As far as I can see, there's nothing an extension developer can do to change this behaviour. I think this new feature will reduce confusion, so thanks again for the suggestion.
I hope this works for you. Let me know if you have any issues with it, or other suggestions.
Thanks,
Richard.