I just looked at the BDP-52FD manual, and heres what I would check.
If you are using L/R stereo out, that should just work. If not, the digital audio out may need to be turned off. Page 42 seems to indicate this.
If you are using digital audio out (Optical - p42, HDMI - p43), it should be set to PCM. This would also be the setting for using optical with an outboard 2 channel DAC.
I had also been thinking about a Downmix function as Edorr mentioned, but page 42 indicates that is on the step up model, BDP-53FD.
Not sure about the secondary audio (page 30), but might be worth investigating.
Hope this helps.