JUki TL 98QE - unwanted gathering fabric but only when trying to quilt.

Question edited for clarity.

Incorrect thread tension. It is a delicate battle between upper and lower tensions. Set the bottom one correctly and then work the top one to put the thread loop in the middle of the fabric.

Quilting is a bit more finicky than regular sewing. Be sure to ALWAYS RAISE the presser foot when threading the top thread. FWIW, I use a separate bobbin case for FMQ that I have tightened the tension to keep the bobbin thread from coming to the top of the sandwich, but I tend to use a finer thread for quilting so adjusting the bobbin takes care of it. In your case, however, it sounds like the top thread is staying under the fabric. I would try tightening the top tension. Also, install a brand new needle--a top stitch, embroidery, or microtex needle seem to work well for me. Test well on a sandwich made of the same fabric and batting and get it adjusted well before sewing on your quilt. Sometimes sewing speed will affect stitches under the fabric, or even on top.

5 Free Motion Quilting Problems and How to Fix Them

Correcting Sewing Machine Tension for Free Motion Quilting NQC

LOOPS Tension or Speed

https://www.generations-quilt-patterns.com/machine-quilting-thread.html

https://www.generations-quilt-patterns.com/sewing-machine-tension.html

https://www.generations-quilt-patterns.com/machine-quilting-tension-problems.html

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You need to drop the feed dogs, install a darning or free motion quilting foot (make sure the presser foot is lowered). Because you will not be using the machine to move the fabric, the stitch length selection is of no importance. Make sure the stitch width is set to zero. You should test FMQ on a scrap quilt sandwich of the same makeup of your project, ie quilt fabric with batting sandwiched between. The upper tension should be set so that both threads meet in the middle of the quilt sandwich. Because it is FMQ, some extra adjustment may be needed.

Once the tension is where you want it, you can practice FMQ until you can move it smoothly in conjunction with the machine speed.

Practicing on a white board with erasable markers is a handy way to learn to move smoothly. The most difficult part of free motion quilting is learning to move the fabric smoothly. Do NOT lack for practice as that is the only way to improve. Those people who make it look simple have been doing it for years!

How to Free Motion Quilt on Regular Sewing Machine

Free Motion Quilting for Beginners Part 1 Video from Sewing with Nancy

Free Motion Quilting

Learn How to Free Motion Quilt Stippling

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When stitching together a quilt sandwich, it is recommended to use a walking foot on your machine. The walking foot moves the upper fabric in conjunction with the feed dogs. Sometimes, if the quilt sandwich is not too thick, a roller foot can also help but may not be sufficient for a quilt sandwich.
What is Walking Foot Sewing Tips for Beginners
How To Use Walking Foot
How to Use Roller Foot

You may also check the presser foot pressure on your machine. This regulates the amount of pressure the presser foot applies to the fabric and the feed dogs. If the pressure is too strong, it will tend to push the upper layers of fabric, creating a bubble look. If the pressure is too loose, there is not enough pressure for the feed dogs to physically pull entire quilt sandwich under the presser foot.
(The pressure is adjustable depending on the types of fabric and thicknesses being sewn.)
http://www.sewdaily.com/how-to-sew/sewing-machine-basics/the-best-kept-secret-on-your-sewing-machine

http://makeitsew.biz/presser-foot-pressure

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Could be several things.

First, install a brand new needle, perhaps a top-stitch needle will work better because it has a groove in the shaft that protects the thread. Make sure the needle is the appropriate size for the thread you are using--a needle eye that is too small will cause the thread to hang or shred. When the needle penetrates the sandwich, the top thread forms a loop. If the eye is too small, the thread will not come back up through the sandwich, leaving a loop under the fabric.

Remove the top thread from the machine.
ALWAYS RAISE the presser foot and rethread from the beginning.
Set the top tension to the midway point and retest your machine on a quilt sandwich made of the same fabric layers as your project.. Tension problems are more evident when sewing multiple layers of fabric, so tweak the tension until the top and bobbin threads meet in the middle of the sandwich.

I don't believe you will have to adjust the bobbin tension, but in case you do, be very careful. Mark the tension screw setting FIRST so you can reverse any changes you make. Bobbin adjustments are made in very SMALL increments. Because I tend to use a lighter weight thread for my quilting, I have a specific bobbin case that is adjusted for my quilt thread and I keep my other bobbin for regular sewing. Then I don't have to keep adjusting the bobbin tension when going from sewing a quilt to something else.

Some machines do better with certain brands of threads than others.

Adjusting Sewing Machine Tension to Prevent Problems

here is a manual for the machine, it shoud have the information
about the tension discs

http://www.google.com/url?sa=t&rct=j&q=&esrc=s&frm=1&source=web&cd=3&cad=rja&ved=0CDsQFjAC&url=http%3A%2F%2Fwww.sewingpartsonline.com%2Finstruction-manual-juki-tl-98qe.aspx&ei=c0alUJ7XMsW7iwLj4YG4Bw&usg=AFQjCNGNGRcwjwIqUsksKufExJXqiQYlOw

Check the height of the quilt under the machine-adjust the bars until the quilt is just barely over the bed of the machine, and level front to back and side to side. Also, level up the frame, using a long carpenter's level. You'd be surprised how much this can help with all sorts of thread problems.

Make sure the needle is in correctly. On most machines the flat part goes towards the back of the machine. Also make sure you are using the correct size needle for the type of thread and fabric you are using. Thicker fabrics such as denim and upholstery fabrics will require a thicker needle, like a 100 (16).

It is recommended that a size 100/16 needle (flat shank) be used for most regular cotton fabrics. Batiks require usually a size 120/18 needle. Hope this helps.

You need to be using a free motion foot or a darning foot, the regular presser foot is not for free motion.