No problem in my situation. If I remember correctly, what you describe (5.1 only) is what happens when you connect a 1.3 amp to both the player and the tv.
I've got a Denon AVR-2310 receiver (so, no 3D-support) and a Panasonic TX-P42VT30 (which does support 3D).
The 310 connects with a 1.4 HDMI to the tv, and the secondary HDMI-output with a 1.3 cable to the amp.
Then in the 310 menu:
- Set "HDMI Audio Output" to "On"
- Set "HDMI(SUB) Output Mode" to "V.OFF(Video Off)"
There is also a menu option to switch off the annoying amber light
Don't forget to set the player to send Bitstream. Et voila, the 310 is then able to send HD-audio to your receiver/amp, while you enjoy 3D content on your screen.