Lonnie,
I used to not mix batiks with non-batikds too. Then I saw Edyta Sitar's quilts on The Quilt Show with Alex Anderson and Ricky Tims. E.S. is famous for mixing batiks with printed fabrics and the results are just gorgeous (IMHO). So now I mix batiks with all sorts of non-batik fabrics as the fancy strikes me and I've never had a problem. I don't know anything about longarm quilt machines. Maybe they have a hard time because I can tell you that handquilting regular quilt fabric and handquilting batiks is a bit of a different experience. The batiks tend to be higher thread count, I've heard. Anyway, don't worry about it.