This is a known issue. I have the exact same problem and I just got answer from Bose:
An issue occurs when watching 3D blu-ray movies through Bose Lifestyle systems (T, V, 135, 235) on the latest Samsung 3D TVs (e.g. UExxESyyyy):
3D video is interrupted every 5~6 minutes, resulting in black screen or split screen for a few seconds.
The U.S. development team is analyzing the issue and looking for a possible fix.
At this moment, there is nothing that we can do to fix the issue. So there is no reason to send these units in for repair.
The only work around for the time being is to connect the Blu-ray player’s HDMI output directly to the TV and an additional audio connection to the Bose Lifestyle system when watching 3D movies.