I have been having the same problems on some larger flat projects such as the card I made for Jaun. However, I was using hardwood, and I think it was poplar when it happened. The part that I cut stayed flat, however, when I painted the backer it started to warp as I was painting it. Now both pages of his card are warped. I even clamped them together, laid heavy books on it and it still looks terrible. The plus side to this? The card stands up nicely by itself.
The Dragon Ball Z pics that I cut were from cheap Luan ply and they did not warp. Whats the deal with that?