Try again, rethread the machine, if it messes up again, CHECK THE TAKE UP LEVER TO MAKE SURE YOUR THREAD IS IN THE TAKE UP LEVER. I use a variety of threads in my machines ( I have two 6600's) one for home, other for cabin. Love this machine. I have never had a single problem with either one. They are real workhorses. I never use Coats and Clark thread.,,,only because their quality is not as good as the other brands. BTW, Your dealer is also suppose to give your wife free lessons on all the functions of her new machine. Getting back to the take up lever....this is the culprit 9 times out of ten. I go to alot of quilt classes and guild quilt ins and this happens all the time with a number of machines. Janome finally got smart and started making their take up levers with a latch on it so the thread cannot slip out once you thread the machine property. It is hard to see the take up lever on these machines, since it does not come out of the top when you turn the hand wheel like alot of machines so, so peer into the slot with a flashlight...you should be able to tell if the thread is in the lever. I hope this is your problem...and this solves it.
TO SOLVE THE PROBLEM OF THE THREAD COMING OUT, THREAD THE LEVER FROM, LEFT TO RIGHT RATHER THAN RIGHT TO LEFT WHEN GOING THROUGH YOUR THREADING STEPS.
Feel free to PM me if you like. I have owned Janome machines for 35 years. Diana in TX