That sounds like an incompatibility caused by the recent Windows 10 update. Please try 7+ Taskbar Tweaker v5.15.0.1 beta, let me know whether it fixes the issue.

Can you post your tweaker options, as well as a screenshot before and after clicking the shortcut (or a video)?

That's a known limitation, see also:

https://ramensoftware.com/7-taskbar-tweaker/comment-page-51#comment-13162

Thank you for the info. I see that it's not detected on VirusTotal:

https://www.virustotal.com/gui/file/91ecd30356cdc1cf65d19034544648b3d40dab52de3d1de408aa48e5455fa6ea/detection

Hopefully, the false positive is removed. If not, hopefully it will be removed soon.

I think that we're talking about different things. Which subdirectories are you talking about, what menus, what "hide"? Can you post a screenshot? 

Sort settings are indeed not saved. That's not a bug, it's just not implemented. You can easily sort the items after a restart via Taskbar Inspector:

You can also configure a keyboard shortcut for even quicker sorting using advanced options, see:

https://tweaker.userecho.com/topics/885-sort-taskbar-items-automatically

Regarding "hidden items", what do you mean by that?

It's fine if it's a suggestion for the tweaker, it's just that you created it as a bug. You can exit the tweaker and check whether it's caused by it.

For now I'll assume that it's unrelated, and will change the status to "idea".

Is that issue caused by 7+ Taskbar Tweaker? It has no functionality that's directly related to that.