"Paper piecing usually gives me square quilts, so I don't think that was the problem."
Paper piecing doesn't guarantee the quilt is square. Did you square up the quilt before sending it off? I'd like to see a photo too. Although I'm not a long-arm quilter they're only able to work with what they've been given and have to assume the product is a "final work" and needs no tweaking-squaring etc. If I were the quilter I'd assume it was ready to quilt if it were sent to me. Now if the quilter were somehow responsible for making the quilt top off-square, that's a different story.