With the amp presumably now optimized for a 3 ohm load perhaps it isn’t happy driving such high impedances in the mid-range and lower treble. Or perhaps the tubes or something else in the amp isn’t well matched between the two channels, and the two channels are trying to put out slightly different signals and are therefore fighting each other to some degree as a result of having their outputs connected together.
This is more than likely contributing to the issue since one amp has about 300 hours on it (and the tubes) and the other new one has about 15.