The problem with vector-DNA is that it jumps not only into the genome when you want it but also jumps out of it and inserts itself into a different organism without any warning (hence the nickname jumping genes). Vectors are totally unpredictable. That's what makes them so dangerous: if you eat them, you may end up with no damage to your own DNA. Or you might end up with a tomato-flavoured tumor.
I have never once heard this suggested even by the craziest of anti-GMO activists. Do you have any citations at all for this happening in humans due to GMO crops?