Are you using a press brake to make flanges around the edges of the shelf piece? I couldn't imagine a shelf being made out of simple flat sheet without incorporating flanges around the edge. Even if you're not using flanges, I don't think that adding flanges will prevent the problem you're encountering.
Here's what I think your problem is:
The punching operation distorts and stretches the material in the middle, but not around the edges. This makes the problem that there's too much material in the middle of the shelf. So, how can you shrink this (slight) overabundance of material?
You might try either of these:
1) Run a weld bead in a large "X" on the underside of the shelf. As the bead cools, it contracts, pulling the material inwards. This is done in the manufacture of safes when a panel is bowed out after the heavy welding around the edges. The large "X" is done on the inside and then covered with insulating material and is never seen. Depending on the amount of initial distortion, I would imagine that your welding techs can get a feel for how long/what size the weld bead would need to be. Though I'm guessing you don't need much. The only issue I can see with this is that it may discolor the top side of the shelf which may or may not be a problem for you.
2) Keep the outer edges of the shelf cool with a copper heat sink or jig or by clamping it with some long flat bar. Next, heat the middle of the shelf with a rosebud torch and use separate supports to keep the shelf as flat as possible. After the middle of the shelf is red hot and well supported, cool it with water or ice or compressed air. You may find that you don't need to do any sort of forced cooling beyond just still air. BUT MAKE SURE THAT IT IS SUPPORTED WHILE IT IS COOLING. What this process is doing is introducing residual tensile stresses in the material. Just make sure that you keep the outer edges cool, get the majority of the inner area glowing red hot and don't allow the weight of gravity to distort it while it is hot.
Either way, you are making the shelf more like a trampoline which is preloaded with tensile stresses before service, as opposed to being like the top of a paint can which will be unpredictable and annoying in use.
If you try #2, you may also go to a local auto body shop, as this is a process that they use to remove minor dents from body panels if the distortion isn't too great.
Engineering is not the science behind building. It is the science behind not building.