I would be one of those folks that connect the DVR directly to the TV. But that aside, you haven't really stated the problem. The Sony quote mentions VOD but claims 3D content is fine.
When you use your CT350, what specifically doesn't work?
Anything presented in 1080p/24 thus far seems to be an issue. When I pass it thru the Sony box, go into the DVR's miscellaneous options menu and look at supported display resolutions I do not see 3D support for 720p or 1080p/24, when I direct connect those resolutions in the menu pop right up.