Comment 1 for bug 1922748

I haven't been able to reproduce, but I have a guess as to what might be happening
If the dialog shows up as "custom" rather than "clipboard", that means there isn't any image on clipboard (which is why the subsequent paste fails). When there isn't an image on the clipboard, Pinta uses the previous new image size from the settings (~/.config/Pinta/settings.xml), which maybe happens to match the size of your screenshot?

I'd suggest trying out the GTK3 build of Pinta to see if that works for getting an image on the clipboard (Pinta just uses GTK for accessing the clipboard)