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We're sorry to hear that your having sound issues. You may try to do a power reset on all devices by unplugging it from the power outlet for about 1 min and replugging it back. You may also want to disconnect and reconnect the HDMI cables.
Ok I think we have solved the problem so for the benefit of others here are my findings:
The HT-RT3 can't handle DTS. It seems to be ok with Dolby Digital however.
To get the sound going I had to change the digital output over the ARC to "PCM". I need to do some more testing on this as I have a feeling my 5.1 setup has just become a 2.1 setup, depending on if the TV can send a 5.1 uncompressed signal over the HDMI.