As far as the system balance being off, try switching the RCA cables on the back of the Emo inputs, then outputs to the amp, if that doesn't fix the problem, try switching the speaker cables to see if that works.
Be sure to put everything back after each step.
The is the box approach to trouble shooting, it will isolate the digital source, the DAC-preamp, the amp then the speakers one at a time.
When you identify the offending component tell us what you find.
Speculation is your amp is starting to fade on one channel but it is just a guess.