Solution:
The output audio device can be selected in the registry of the i.MX31 PDK Windows CE 6.0 BSP. For more information, please refer to the Section 4.4.6.2 "Optional Audio Driver Runtime Configuration Registry Settings" of the "i.MX31 PDK Windows Embedded CE 6.0 Reference Manual" (pdk13_imx31_WinECE60_RefManual.pdf) document, included in the BSP documentation bundle.
Also, please refer to the PMIC_AUDIO_OUTPUT_PORT enum definition, that can be found in the
%WINCEROOT%\PLATFORM\COMMON\SRC\SOC\FREESCALE\PMIC\INC\pmic_audio.h file. So, for the [HKEY_LOCAL_MACHINE\Drivers\BuiltIn\Audio\PMIC\Config\Playback] key, please try to use various PMIC_AUDIO_OUTPUT_PORT enum values. In particular, please try to use the value of 0x100 for "LeftChannel" and 0x200 for "RightChannel" instead of current 0x40 and 0x80.