This is so interesting - I've just had this experience the past few days working on a Bargello. On my Baby Lock Crescendo, the quilting stitches set to a default of 2.0, but on utility stitches the default is 2.5. So, I used the quilt stitches (to get 1/4 seam) but I moved the length up to 2.5. I sewed all the segments together and after cutting crosswise to get the strip sets together, guess what - the seams were separating an the ends. Once I noticed that, I have had to go back (2.0) an sew several ends together again. It has been so frustrating. Yesterday, I started using Elmers glue to match up seams so I don't have to handle the fabric so much. That has really helped. So lesson learned - trust the machine's default settings.
For me, anyway.