It looks like version 4.6 went to ffmpeg for transcoding and it doesn't work with WMA Lossless, I did the following to restore transcoding of WMA Lossless for now.
- Make sure you have wmadec.exe and lame.exe in your transcode directory (Should be under your SubSonic folder, mine is C:\subsonic\transcode for example.) You should still have them if you upgraded from version 4.5, otherwise you should be able to find them online.
- Go to Settings, Transcoding
- Remove wma from Convert From box under the mp3 audio entry
- Under Add Transcoding add a name (wma for example), add wma to the Convert From box, mp3 to the Convert To box, "wmadec -b 16 %s -" (without the quotes) to Step 1 and "lame -b %b -r - -" (without the quotes) to Step 2.
- Select Save and enjoy.