ditto ditto ditto to all the good suggestions already given.
I got my 6600 in September, so just ahead of you ... and have not had any problems of this nature. Nor with my preceding three Janomes! And believe me, I have sewn miles and miles since I got my 6600.
Just ahead of that, I discovered Aurifil thread ... and started to use it. I heard/read all the horror stories about it being a thread diva, so decided to stick with the Aurifil. And it's been clear sailing!
I tpo had LOTS of Gutterman threads, some Mettlers, but it's hard to go back, once I tried the Aurifil as it makes a much nicer seam! Now that I am more than familiar with the 6600 and know there's no problems ... I have been using my Gutterman stash, and so far, no problems! xxxxxfingers crossedxxxxx!!
With all that's been said, I think your best tip is to buy that one spool of Aurifil (or whatever your dealer recommends) ... and give it a try. You have mentioned that your dealer has offered that as a solution, yet it appears you have not taken that suggestion. You can prove them right ... or wrong! If right, then the problem is solved ... if wrong, then let the dealer figure out the solution.
Being that it's working just fine when you take it to your dealer ... it would appear there is indeed something different happening. Are they using your thread? Are you doing any of the sewing? As already suggested ... sit and sew along with your teacher/dealer ... and perhaps there's some little things you are missing when you are home and DIY which are causing the problems.