I've been using PS3 MS for years with my original PS3 and ripping dvd/blu ray to MP4 via handbrake using the 'Normal' profile and PS3 profile in the older versions of Handbrake. Never had any issues at all.
At the weekend I purchased a E5 series Panasonic Viera and I've encountered some strange behaviour. PS3MS sees the renderer and my folders and files appear fine but only a handful will actually play. Others just get the 'Please Wait' then 'Cannot play file' message. The server is connected via wireless with the TV plugged straight into router. PS3 plays them all fine. All the rips are the same so why would this be happening? I've tried A few other media servers (serviio, twonky etc and its the same). Don't really want to transcode as I'm on wireless and I don't think it'll cope.