The "delay" is only 0.5s so thats not the issue here.

Do you have both apps and the panel files in the same directory?
Do you start panelapp from Ambient, Shell or some other way?
Any fails showing up in Snoopium when trying to start the prefs?

What is kinda wonky atm is that panelapp does not use an assign or even PROGDIR: to start the prefs it constructs a full path from panelapp's path, calls AddPart(buffer,"PanelPrefs",300); and then Execute().
Thats just for the moment as in a finished product it would need to call into Ambient to make it load and bring up the Panel prefs pane.

Starting PanelPrefs without PanelApp running should result in some 0-Pointer accesses as it would fail to open "panel2.library" (against which I should test and have it fail with an error message).
If you have for some reason more than 1 PanelApp running (which won't be possible in a "release" build) PanelPrefs would still connect to the 1st (which would be hidden behind the 2nd ones panel windows).


So please run Snoopium and also look into debug output of which I might add more if the issue persist.