Hi Lucy, I am sorry you are having these problems.
I have heard some people have a hard time with the generic plaq (nothing to do with gluten free diet tho), maybe trying the brand name for a month and see if you continue to have the same problems. I've been on a gluten free diet since 9/03 and on Plaq (generic) since 3/04 with no problems.
It is also very possible that when your lupus is flaring it may affect your GI tract. Also, do you eat a lot of dairy? I have noticed if I am in a lupus flare and my gut isn't right and I eat dairy, it's almost like I've eaten gluten.
I hope you can find some relief soon!