Exactly as I had suspected, 2.3.13 doesn’t support PlayOn so it runs Comskip always. 2.5.4 does support PlayOn AdSkip so it uses the embedded ad markers and skips running Comskip.
If you prefer to have 2.5.4 not use the embedded ad markers from PlayOn then you can disable that option in Conversion Task -> Expert Settings -> Check chapters for Ad markers and it’ll run Comskip instead.
