That does not seem correct. Have you checked your settings in your PS3? I don't have a PS3 but there are several sound options on my Sony Blu-ray player of which one includes downmixing. I found that it was necessary to get the settings correct or else the Sony BD player did indeed mess up the sound (for example movies came out as stereo).
You are correct that "re-clocking should have solved of the problems." So I would suspect something else. One possibility is that the PS3 being a high powered computer might be inducing a lot of noise on your AC power (switched mode power supplies are notorious) and this might affect the DAC through its own power supply.
FWIW I use a power conditioner and keep my computer equipment well away from the audio gear (on a separate conditioner in a separate wall socket).
You are correct that "re-clocking should have solved of the problems." So I would suspect something else. One possibility is that the PS3 being a high powered computer might be inducing a lot of noise on your AC power (switched mode power supplies are notorious) and this might affect the DAC through its own power supply.
FWIW I use a power conditioner and keep my computer equipment well away from the audio gear (on a separate conditioner in a separate wall socket).