"the boards have shrunk unevenly, so that some are significantly bowed and are trip hazards."

This is indicitave of improperly fastened deck boards, and or bad ventilation. Correctly fastened decking will not move in that direction. A well-vented deck will flatten itself out as the wood reaches a stable moisture level.

What method of decking attachment is used? This can be fixed in many cases, different ways are possible, but it depends on how they are put down.

What kind of air circulation is going on under the deck? Is it close to the ground? Are there vents in the perimeter facing?

This time of year is when the deck will look it's most wetahered. As the wood dries out it's surface opens and you really notice lots of little checks and cracks everywhere. Don't worry about this. It is a natural process that looks the worst for the first few seasons, but gets less noticeable as time goes on. The gray color takes time to develop evenly. You could try a good cleaning to remove the mildew, but it will also remove some of the gray. Using a cleaner like EFC-38 would lighten the wood and even out the color. Over the summer the wood will return to gray, this time more evenly.

Thank you very much for the reply. I will have to look into EFC-38. Should this be scrubbed with a brush? Low-power pressure wash? By lighten the wood, do you mean that it would take it closer to its original reddish-brown color? (Sorry if these q's are obvious.. I don't know anything about decks :)

How aggressively can we clean it without getting rid of the gray? For example, would a simple hose and scrub brush be abrasive enough to expose brown wood?

As far as the deck construction, the ipe boards were first fastened to each other, then laid in large floating panels on graduated pedestals over a slightly sloped waterproof membrane. So there's probably somewhat limited air circulation. We have two young kids, so I'd love to even the surface out once and for all so I don't constantly have to worry about trips.

Thanks again for your help!

"the ipe boards were first fastened to each other, then laid in large floating panels on graduated pedestals over a slightly sloped waterproof membrane"

Ah-ha! That is the problem. The construction style and methods are totally unconventional. Ipe must be fastened to joists, or in your case sleepers. If you had described the construction method before building, I and many others would have told you right away this would happen.

Wood decks should be constructed with long continuous members. Short boards move more. Since the deck is essentially floating on raised stantions, there is no way for gravity alone to keep the surface flat, as the wood moves with the seasons. There is no way to get the surface to even out "once and for all" It will continue to move and do this forever.

If you can replace the stantions with sleepers, and then fasten the panels directly to the sleepers, screw each individual piece of decking to each sleeper with stainless screws, no pilot hole drilled into the frame, just through the decking, you might have a chance of saving this deck.

Don't do anything else until after you have fixed the framing correctly.

Flipping the warped panels over to let the sun dry out the bottom side is a good way to get them flattened out naturally. Once they are flat, screw them down!

Use short trim head screws, 2" max length. Longer screws loosen up more as the framing dries out, because they are sunken deeper into the framing, A deck screw with 3" embedment will pop up twice as high as one with 1.5" embedment. Therefore shorter screws hold better for decking.