However, when I click on the .app icon, the icon bounces in the system 
tray, then closes, and, after about 15 seconds, re-opens.

It’s a side effect of --onefile mode combined with --windowed mode (or the 
.spec file equivalents). Because a onefile executable is an executable 
within an executable you get a bouncing icon for the outer executable which 
disappears when macOS realizes that it’s not really a GUI then the inner 
executable launches which creates a new bouncy icon. The fix is just not to 
use onefile mode which is fairly useless combined with windowed. It should 
boost your startup time too.
​

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