Your plate is relatively long and thin, and Aluminum (even with T6 temper), is not particularly stiff or strong. That said, typical bead blasting or shot peening should not deform it.
When anodizing, a bunch of electrical current is being pumped into your part, since it is relatively large surface area. In order to prevent arcing of the electrical current, it needs to be clamped or otherwise held securely to the rack used for the anodizing process. Depending how it was clamped (and what kind of warping you're seeing), this could be the cause of your problem.
I'm not sure how badly warped it is, because I'm not sure what your tolerances on the flatness of the plate were, and therefore by what margin it is warped. If you're holding relatively tight tolerances for flatness (less than, say, .010"), shot peening or bead blasting prior to anodizing is a good idea.
In summary, I'm thinking that whatever non-flatness was in place prior to anodizing, plus any additional warpage that was incurred in retaining the plate to the rack caused some bending or warping. When the anodizing was applied, it 'locked in' this warpage, and now your part is more warped than before.
Aside from the obvious possibility of them simply mishandling your parts, I don't think the machine shop or the anodizing shop did anything out of the ordinary. You may just have to make your plate a bit thicker if possible, or control the flatness tighter to begin with (again, not sure how badly out of tolerance we're talking here), or have a discussion with the anodizer about your problem to see if they can process it differently next time.