This is a problem with the renderer file and can be fixed by doing the following:
Locate the PS3.conf file located in the renderers folder of your PMS installation folder (Usually "C:\Program Files (x86)\PS3 Media Server" anymore).
Open PS3.conf in a text editor such as Notepad or GEdit.
Scroll down to "TranscodeAudio =" and add LPCM to make it absolutely the default audio codec used for transcoded audio.
(Optional) Scroll down to "ChunkedTransfer =" and add True to the end of it. Not necessary, but it makes the data being sent more honest to the PS3.
(Optional and controversial) Scroll down further to "DLNAOrgPN =" and add True to it as well.
Finally, the one thing that makes FLAC work.
Scroll all the way down to the bottom and replace the supported audio section with this which comments out the wav format and replaces it with what is actually supported as-per the PS3 manual. Bear in mind that I have not tested this with 6 channels, so it may need to be reduced to 2 if you have trouble playing 5.1 audio:
# Supported audio formats:
Supported = f:lpcm n:6 s:48000 m:audio/l16
#Supported = f:wav a:dts|lpcm n:6 s:48000 m:audio/wav
Supported = f:mp3 n:2 m:audio/mpeg
Supported = f:aac n:2 m:audio/x-m4a a:(?!alac).+
Supported = f:wma n:2 m:audio/x-ms-wma
Supported = f:atrac n:2 m:audio/x-oma