troubleshooting for a lost channel

Start by reversing (left output to the right input) cables from the TT to the pre. If the problem moves to the other channel it is the TT or cartridge. If the problem doesn't change put those cables back and reverse the cables from the pre to the amp - then the speaker cables.

Now that I re-read your question and it only happens with the TT That pretty well says it all. It's either a bad cable or cartridge. If you swap the right and left outputs of the cartridge you will know it is the cartridge or tonearm cable or something else related to the TT