PuTTY Portable / instance limit / session list only in first PuTTY window

Dear all,
I find myself using more and more linux hosts in my home network. I use PuTTY Portable to manage them. Which works great so far.
Only one instance can be started, so I use right click onto the title bar and "new" or "duplicate session" to open up multiple sessions.
One sometimes very annoying problem is that it seems that PuTTY Portable deletes the temporary registry settings when the first window closes, no matter, how many PuTTY windows are open.

Example:
1.) start PuTTY
2.) login to host 1
3.) right-click onto title bar, new, pick a different host, connect: 2nd window comes up
4.) close window 1
5.) right-click onto title bar, new: session list is empty.

Workaround: close window 2 (and, if you have, all remaining other PuTTY windows) and start PuTTY from the PA.com Menu again.
Right at the moment, for example, I can't close a window, because I am running an interactive dist-upgrade. I can't start other sessions either, because earlier I closed the first window.

Is there any possibility that the PuTTY Portable starter can leave the PuTTY setting in the registry as long as any PuTTY window is open?