Are you using Balsa wood or Bass wood?
Bass wood is pretty stable and takes stain well with little or no movement. Its what they use for intricate carving, wooden boxes, venetian blinds, musical instrument components, plates and some architectural elements.
While its grain is somewhat noticeable it is pretty smooth and clear.
Balsa wood is a soft wood that you see in alot of the hobby and craft markets. It has several types of milling grades and the most common (like the sheets we see in the hobby shop for doing diorama work etc.) are "A" Grain. This is usually milled into sheets and has long fibers that show up as long grain lines. It is very flexible across the sheet and bends around curves easily. This flexibility and the way the grain runs makes it warp very easy. It will have a "soft" or velvety feeling to it.
Warpage is usually the result of wood drying at different speeds along the grain causing one side to contract or swell fast than another. This can result in warping, skewing, chequing, or even splitting.
On another note, regardless of which type of wood you used,
Did you only polyeurathane one side or both? (one side only will not have grain movement on that side, with grain movement from moisture absorbtion on the other, the resltant tension will make your wood happy)
Did you eurathane the ends too? (A place for moisture to absorb. its why furniture wood suppliers wax the end grain of hardwood lumber)
How may coats of eurathane did you use? (Balsa and bass are both "open" celled woods, meaning that the cells lose their water and this leaves large celular voids that give the woods its rigidity as well as its lightness. Fail to fill these up and they will absorb moisture differently)
How dry was the eurathane before you added your spackle? If it was still damp, then moisture can get through.
If you are "spackling" over bass or balsa wood to make a wall for a building, you be better served by using something like foam core, gator board, foam sheet, or even thin ply, ply wood to use as a wall core. these are more stable and you won't have nearly the trouble with warping.