Firstly the problem is not just fixed by using PS3mediaserver. You have to output the audio from the PS3 by using the optical cable and into an amp that has the ability to decode DTS sourround sound.
There is a setting in PS3mediaserver for Cinavia (the latest version as far as I know) but this will not affect anything if you have not got the correct equipment.
This only works on the PS3 because the audio chip that decodes through the optical output bypasses the cinavia chip, all other audio outputs IE. HDMI, Phono etc.. still go through the cinavia chip.
There have been reports that in the newer PS3's this has been fixed, some even suggest it's been fixed in the latest firmware updates.
Up till very recently I used my old PS3 for playing all my media and have never seen the cinavia warning, I've always used the optical out. I recently stopped using the PS3 as it's dying and I bought a stand alone media streamer/NAS which doesn't seem to have a cinavia chip in at all, I'm not using optical audio on this box and have not seen the cinavia message yet.
My m8 was using a PS3 slim, bought around 2 years ago, and up till recently has had no problems with cinavia, but since firmware 4.10 he has seen the cinavia warning a few times, even though he hasn't changed any audio connections or the version of ps3mediaserver.