Should there be anything showing? Like, do you have an active download that is supposed to show up there? Or is this a Windows issue with the app showing to exist in task bar, but not popping up, when selected? I have this sometimes with explorer folders when returning from standby. I cancel them with right mouse button in task bar.
I do not use the itch app. And I would not know, if I could use my custom css there, as I do not like scroll bars, as they take up valuable screen space - and with dark theme they break the color scheme.