I've started seeing this behavior as well. Also newly opened tabs don't always show up in Sidewise's list. Basically, Sidewise's list of tabs is in every way out of sync with reality. It has been this way for a few weeks now, making Sidewise pretty much unusable.

Is there some further debug info I can provide?

In my view, Firefox's Tree Style Tab is pretty perfect, and the reason it's better than Sidewise, is because Sidewise uses a separate window, rather than integrating into the browser window, and all the side effects that difference brings. Different keyboard shortcuts between main browser window and Sidewise window is one such harmful side effect. Ideally the shortcuts should be more or less identical, including certainly ctrl+tab, which is one of the more important ones for some users, like myself.

Framed that way, I view this shortcut as very natural one in making Sidewise approach its goal of not coming across as a separate window.