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I think I know what's going on, all issues are non issues except for the icon not displaying in the notification area when autostarted with the system.

I reinstalled 0.5.5, and set it to autostart via XFCE Settings/Session and Startup/Autostart. I testing the setup with another app first and that launched when I rebooted and logged in. So I set one up for qjackctl, rebooted and logged in. I did not notice the icon in the notification area. I then launched a terminal and did and "htop" and filtered for qjack. I noticed qjack was running but no way to open it up. I killed the process and launched qjackctl from terminal by typing in qjackctl, and it launched and put the icon in the notification area. I quit the app and launched it from the menu and it put the icon in the notification area.

It seems that only when it's auto started on system login that the icon does not display in the notification area, which worked perfectly in prior versions.

Any ideas why 0.5.5 won't display the icon in the xfce notification area when the app is autostarted from system login?