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Hello Colin,
with default PS3 settings, the Hub sends a sequence of button presses to Remote Buddy when you tell the Harmony to turn off the devices. Since the PS3 has no dedicated power off command, my best guess is that the Harmony tries to enter and navigate menus here to turn off a PS3.
This can/will lead to unwanted effects like the one you observed.
You can avoid this by making the adjustments outlined in the official HowTo, Step 3, "Tweaking power settings":
https://www.iospirit.com/blog/article/184/-/
Cheers,
Felix