A little background on what is happening with the handshaking might help. When your TV is connected directly to the Denon, it sends a signal called an EDID that contains information about the sink (the TV) and what its capabilities are. This is then taken by the Denon, the information in the EDID is changed based on the Denon options that you selected and that modified EDID is passed to the source device. The source device then takes that information and generates an audio and video signal that is compatible with the information received from the sink (and modified by the Denon).
Now when you add the splitter after the Denon, the additional complication becomes that both sinks are sending separate EDIDs to the switcher. The switcher then has to either combine or choose one EDID to forward on. There is no standard way of doing this. So, every distributinon amp (splitter) can choose their own method. Just as long as the resulting EDID is valid and should include only capabilities that both sinks have the dist amp has met the HDMI spec. If only one sink has 3D, then the EDID sent back says that the displays are not 3D compatible because both do not have 3D capability.
So, the two possibilities I see is that the splitter is having problems reconsiling the two sinks or the Denon is having a problem handling the EDID that the splitter is creating and forwarding on. I suppose the other possibility is that this is just the way that particular splitter works. You haven't said if you tried to bypass the Denon with the splitter and what happens then. That could be a good clue.
But either way I suspect if this problem is bothering you, the best method to solve it would be to try a different splitter with different firmware. While on the topic of firmware, also make sure your TVs and the Denon have the latest firmware. It's usually impossible to update a distribution amp's firmware except for some that are in the $150+ range.