Hi, and thanks for feedback. I don't understand exactly what exactly it's happening in your case because saving multiple windows definitely works. Not sure if there can be any other addons that can cause such an issue but saving definitely works ok. Of course... there can be lots of things that I can't control that can affect the addon but the code does exactly what it's suppose to. I will investigate to see if I can replicate this but I can definitely say that I never seen encounter this kind of bug.
The addon may not be for everyone and I do get that but please understand that your experience with it most probably is not reflection of the addon quality. 99.99% of the time the addon works as it should I would say. If there are serious issues that I can tackle (like the one you've mention) I will try to fix them as soon as possible but in this case I simply have no lead what exactly causes Firefox to stop saving the second window.
If you are able to provide more information that would be helpful (I usually don't test everything on linux and I don't have a Mac so if it happens to be one of these 2 I might have a better lead) please send me an email. Of course, I will still try to figure out what may be the cause for this issue.