In Xpad 5.7 the deprecated libappindicator has been replaced with another app indicator, resulting in different behavior of the systray icon. The left mouse click on the tray icon does not work anymore, to my annoyance as well.
Which version of Xpad where you using on Pop!_OS and which version are you using now on Arch with Gnome?
Currently running Arch with GNOME. Had this working before with Pop!_OS