Ok.........I don't know if I'm going to explain this right.........but when you thread your machine starting on top....
then bring your thread down and around to go back up to the uptake arm and instead of bringing the thread
around the uptake arm from the right to the left bring it from the left to the right then straight down so that it will
cross on the way going down to the needle area, you won't be able to see it crossed. My girlfriend has a Janome and
she was having trouble with her automatic thread cutter also so the women at the store where she got it told her to
try that and it worked............no more trouble and it works and sews fine!!!!

I know what you mean, but the Janome cuts the threads quite short. In fact, with some poly thread I have found that a needle down might unthread the needle because it is so slippery - but that might also be I was not using proper spool holder...

I use leaders which solves the problem unless of course you are in the middle of the seam line! I also use the up-down-up with tweezers if I need both threads on top of the fabric.

For those who think it is better to cut with scissors...I am using an older machine now while Janome in shop, doing paper piecing, and I am a thready mess!!! I have to hook the threads into the upper manual thread-cutter, do the seam, than hook them over and cut on the thread cutter, then take the piece and nip off the four threads...no threads to cut at the end of every seam is worth the money IMHO! If anyone has a better idea about how to cut threads without a thread cutter, love to know!

I have a Bernina with a thread cutter. I also bought this model to have a thread cutter. I had the same problem with the thread knotting. My dealer told me to always be sure to remove my fabric to the left side. I don't know why, but this solved my problem - just always remove the fabric to the left.

That is not an acceptable answer!! I'm considering buying a new machine and the thread cutter is on my list of "Must Have".

I have a small Brother that I take to workshops and having all those extra threads drives me crazy. The machine I use at home has the thread cutter and I love it.

I am not sure but I think I get it; when I've cut my thread with the cutter the next seam does often have a little wad where the tails got sewed back down into the seam. Is that what you mean?

I don't think the cutter is working wrong, I think that's just how it goes when you have small tails left over. Larger tails hang out and out of the way, but the small tails have nowhere to go so they get caught up in the stitches.

Leaders/enders would solve that; chain piecing would solve that; pulling the tails longer would solve that... I just leave it and then when I'm cleaning up I use my needle-nose tweezers to tug the ends out of the stitches and I snip them off if it's something that'll be visible. If I'm quilting I always start as if I'm FMQ'ing and bring the bobbin thread to the top and pull it long so I can tie a knot anyway so it's not an issue there. If it'll be sewn over or hidden I just leave it; it doesn't seem to cause any problems as it's not really lumpy. If anything it's probably a nice secure "knot"!

Wow, a lot of money for something you were told not to use. Yea, that is not acceptable.

I use the thread cutter only when I am doing embroidery

Keep trying
 

Sometimes it is a matter of talking to the right person. This has happened to me with various problems. Sometimes the right person can sit down and fix it easily. Don't give up! Good luck.

I have only been sewing/quilting about a year - I typically use a small scrap leader, chain piece… and FMQ… I am curious to learn when using a thread cutter would be desirable. I like to tie off and bury my threads if I am FMQ or top stitching (I backstitch to secure, then go on a small bit, stop pull long threads, cut, pull up bobbin, tie off and bury)…
Someone mentioned paper piecing- I can see it being very useful there… what are other instances that its good to use?

I do not have that particular feature on my Janome 4000, but since this is a feature I would like to have should I ever upgrade my machine, I would be very upset that it doesn't work to your satisfaction. I would keep complaining until I had a satisfactory conclusion.