One more possibility: detach and clean all the connections in the analog portion of your system. Dirty connectors can lose conductivity in ways which vary with the frequency and amplitude of the musical signal.
That sounds like what your experiencing. We've experienced it too and cleaning our phono cable leads and phono stage inputs solved the problem.
That sounds like what your experiencing. We've experienced it too and cleaning our phono cable leads and phono stage inputs solved the problem.