Yes!! Some threads are very linty and it seems that they react different for some of us. Here in moist Seattle I have different issues than my friend in Phoenix. Like, when it is really humid outside are the days I'm most likely to have to change my thread tension from what it was the day before.
Typically I scrap piece and will use two different colored threads, say camel and slate for top and bottom because both of those blend and (with my vision issues) it really helps me see the stitches/problem easier.
Short form: sometimes it helps to know which lint is collecting in the bobbin case. From your information, it may indeed be the entire bobbin casing and that is a pretty simple switch out once they have one in stock.
I've been quilting for quite awhile now and for my first couple of decades, I used Coats & Clark Dual Duty for piecing, top/bottom thread and for quilting as well and had no problems. About 10 years ago I had access to a friend's long arm and first started using different threads top and bottom. Her machine could not wind a decent bobbin so we started buying prewound, our lives got so much better. I found the Coats and Clark "Machine Cotton Quilting" thread to be terribly linty and you start understanding and appreciating things about "Egyptian long fiber".
A couple of years ago a friend gave me her modern Bernina she replaced with the warning that it was picky about threads but seemed to like Aurifil, so that's mostly what I've been using. For the past year I've been running sort of a test using Superior So Fine as my bobbin thread for piecing (previously used on the long arm for quilting) and all in all, I'm pretty happy with the results from ease of work, to stitch quality to lint production.