AutoSkip was broken in the last 'over the air software' update, version 1.1.10600. Thankfully there is a newer update available that fixes AutoSkip and also fixes some other related bugs where the Skippa could stop updating from IceTV (affecting the guide and recording schedules) .
To download software version 1.1.10604 and view the instructions on updating the Skippa using a USB stick or thumb drive click here.
If your Skippa already has software version 1.1.10604 installed try rebooting the Skippa from 'Menu > Settings > General > Restart', or pull the power cord out for 10 seconds.
Note: The Skippa is unable to process the AutoSkip on recordings from any new channels that are broadcast in MPEG-4. Channels currently broadcast in MPEG-4 are ABC HD, 7HD, 9HD, Ten HD, NBN HD and WinHD. Some other channels like 7Flix, 9Life or The Food Network may also be unable to be processed for AutoSkip if they are broadcast in MPEG-4.
If your Skippa already has software version 1.1.10604 installed and only certain channels' recordings won't AutoSkip see the work around described here.