To absolutely clear, I understand that you run the leads from the tonearm into the primary side of the step up transformer, then the output of the step up transfer feeds into the MM input of your preamp.
Is there enough gain from this configuration? Are you listening mostly close to full volume on your volume control setting or at the opposite end of the volume control range? This might tell us something about whether you have problems with too little gain or possible overload of the phono stage.
If you try bypassing the use of the step up transformer (going straight from the tonearm into the MM input), there will probably be insufficient gain, but otherwise, you don't have to worry about doing any harm. If the sound is better, you have an issue with the step up transformer. In the sound remains the same (albeit softer), then you might have a problem with the MM phono stage or the rest of the preamp. If the preamp sounds good with other sources playing into the other inputs, that would me the phono section is suspect. How does the M6 sound with other sources?
If you can take the M6 and step up transformer to your dealer, you can try it there to see what things sound like.
Apart from gain/overload issues, most step up transformers sound reasonably good even when there is not a theoretically ideal match in terms of cartridge source impedance. A really bad, thin sound suggests a failure somewhere and not just a mismatch of components.