Thank you to everyone for your thoughtful comments. I'll post when we have corrected the problem.

Have also had this issue with my Tin Lizzie. I found the problem to be either the encoders (wheels) not connecting firmly on the tracks and not turning correctly. Also if the foot is too high for the thickness of the sandwich it skipped stitches as well. Hope you can fix this as it is a real pain in the neck to deal with.

I purchased the same set up as yours, the megaquilter on the same frame. After some practice on it, it started to skip stiches, with mine it was the stitch regulator sensor wheels. While moving your machine, watch your sensor wheels if you have a stitch regulator on your set up, if you see them pause (or skip) you'll have skipped stiches. I cleaned and oiled the ones on my set up and it solved the issue. Good luck. Hope you get it figured out.

Dunster is giving some excellent advice. I'm not familiar with this specific machine, but you might want to check on their website for any videos on maintenance--if the needle is actually punching holes but not stitching, then it's likely one of the things that Dunster mentioned.

Along with all these great suggestions to try, make sure your bobbin case does not have some lint caught in it. Take a pin and run it between the bar (don’t know what it is called) and the case that has the screw in it.

First..turn off your qbot ..this is a machine problem, you need to get your machine right before you use the qbot with it. I hope you know where your bobbin tension was before you got in there and adjusted it. You didn't say if that made things better or worse, or no change at all. An occasional long stitch or a few shouldn't have had anything to do with bobbin tension. Are the long stitches happening when you sew a straight line or just on curves? A pic of the stitches would help...but I am leaning toward the poster that suggested your top may be too tight. Many new LA-ers want that top tight as a drum. There are a million you tube videos on how to load a quilt..try to watch the ones with your machine first, but basically they are all very similar. Facebook and Yahoo both have groups for megaquilter and qbot, when you get that far. It's frustrating, but hang in there, you'll figure it out.

I agree with intoquilting; my machine doesn't like King Tut thread either. So I've switched to Glide and it's sews like a breeze. No issues whatsoever. Good luck.

I previously had a Tin Lizzie and I believe the same company may make Qnique. In the months I had that machine, I had to replace a circuit board and two stitch encoders. When the stitch encoder needs replacing, it does exactly what you are talking about. It skips direction. You can find out which encoder it is by if the stitches skip when stitching horizontal or when stitching vertical. You may have to call technical support to find out if it is the encoder on the right side of the machine or on the encoder on the left side of the machine. I personally think this is the problem with your machine.

Check how the needle is inserted into the machine. Maybe you have the needle backwards? Or going the wrong way?

I also second the recommendation to check the height of the foot in relation to the quilt sandwich, if it's too high you will get skipped stitches.