I have a similar issue. Have you resolved it?
Two comments about your conf file…..
I think you need to specify the program to use for server side conversion. I believe this may be the line which is commented out in your file.
# ssc_prog /etc/mt-daapd-ssc-script
Also, I think you need tospecify the actual plugin names in the plugin directory………
plugins = rsp.dll,w32-event.dll,ssc-ffmpeg.dll,ssc-wma.dll
But even with doing that I cannot get FS to convert Flac for streaming over a browser.