At first I thought I could replicate your issue but in then when trying to carefully to repeat my steps so I could document the reproduction steps I discovered that a pinned portable worked fine…
What I would do is to first unpin Notepad++, make sure no instances of Notepad++ are running, and then start a portable copy using however you normally start portable copies.
Once the portable copy is running then save a copy of Notepad++'s debug info in Microsoft Notepad. Then right on the Notepad++ on the task bar, pin it, and close/exit Notepad++ to have just the pin showing.
Do not start Notepad++ using the pin just yet. Instead, right click on the pin for Notepad++ in the task bar and right click the “Notepad++” at the top of the menu that shows up, and then left click on Properties. It defaults to the Shortcut tab of the properties and is in the Target field. I don’t see an obvious way to add the command line and so appended the command line parameters I wanted to the end of the Target field.
Save that to the shortcut and start Notepad++ using the pin. Get the debug info again and verify that the path and command line exactly match what you saved when you had first started the portable copy.
I had two strange things happen when I was trying to replicate. One of that was when copy/pasting the command line parameters I needed that the “quotes” around became unbalanced. It caused Notepad++ to try to create a file named “-multiInst” which I declined. I don’t know if I made a mistake or Windows did did something to unbalance the quotes. The result was when started Notepad++ that I got some odd behavior that seems much like what you saw. That’s why I’m suggesting to first get the debug info, then to fix up the Target, and them to re-verify the debug info once I have started Notepad++ using the pin.
The other strange thing is that I normally use an installed copy of Notepad++. In the process of testing pins all of the session/tabs from my portable copy ended up getting appended to the tabs/files for the installed copy. My installed copy is single instance and the portable copies are normally run with -multiInst. As pinning does not transfer the command line I had first accidentally started a portable copy using my new pin without command line parameters. That started the portable copy in single instance mode and I suspect Notepad++ has some instance sharing stuff that resulted in my portable tabs/files getting appended to the tabs used by the installed copy.