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I had the same problem. I had manual season passes set up on one of my Series 3 units to record The Daily Show and The Colbert Report. It looks...
After my TiVos connected today (one Series 3, one Series 2 and a DVD TiVo) they all see WUCW again.
My guess would be that the problem is actually with the disk format you are using. Some formats can't handle files over 2GB in size.
This sounds about as fully baked as the TiVoToGo rollout.
Any idea when (or if) WPA will be supported?