Jay,
Yeah - I realise what you're saying and it is not moisture or anything like that. (Well, not that I know of...)
It is the same thing that happens when you put a cover over your mobile (cellular) phone. The middle of the screen will usually look like that. this is because it is in direct contact with the plastic cover whereas at edges aren't. (due to the rim around the lcd). I have a colour screen phone and it is only really visible when the screen is black and not back-lit. (i.e. - it's 'screen-saver'.)
When it is in colour (even when the screen is dimmed - i.e not backlit,) it does not happen. It is visible, but only just and viewed at the right angle.
*Perhaps* another colour, other than black would reduce this effect.
Of course, the problem also stems from the lexan being warped. It is obviously not sitting on your panel entirely flat. If the bolts holding the lexan on are not as tight as the buttons and/or joystick, then this is likely to happen. As mentioned, there is no need to have the buttons too tight. I think this will be the best solution.
Perhaps you need more bolts holding in the lexan. If there is just one in each corner, a few across the top and bottom may solve your problem.
The lexan will stick to any nice smooth surface. In the case of my phone - this means the screen. (even though the cover is obviously not lexan.) That is another thing to think about - if both the Lexan and the surface below it were pefectly flat and uniformly smooth, then this would not occur. It would be (depending on the smoothness,) either all like that or all like the rest of your panel.
Because lexan is rather flexible, it is bending in this case. Thicker lexan would not do this as much.
Well, not being two cents so much as several dollars, I will leave my opinions with you to think about.
gb.