-- Last Updated: Jan-27-13 3:03 PM EST --
I like the idea of the outwale being too long, but I think it's also possible that it's the inwale which is too long. Which one is too long depends on the actual stress that's going on. Is the gunwale being forced into a sharper curve than what's natural for it? In that case, the inwale is too long. Is the gunwale "trying" to assume a sharper curve than what's actually there? In that case, the outwale is too long. Either way, the screw connections toward each end, away from the separated section are supplying most of the stress, and you probably have to re-drill screw holes that are well outside of that separated section, but only while the gunwale is clamped AND properly curved. You probably understand the reason perfectly well.
Anyway, just to illustrate the idea of a too-long inwale, hold two sheets of paper together, flat, and edge to edge, then bend both of them into a continuous, sharp curve but without allowing any "slippage" at the ends. You'll see gaps open up between them along the curve where the inner sheet buckles due to being too long, but those gaps will will disappear if you let the necessary slippage between sheets occur, effectively shortening the sheet on the inside of the curve. I've never assembled gunwales "from scratch" (with new, undrilled pieces), but to me it makes sense that it should be done starting from the center and working outward toward the ends, while maintaining the proper curvature as new holes are drilled and screws installed. I also think it would be best to do this progressively the same on both sides of the boat, rather than doing one side first (wouldn't it be difficult to duplicate the same amount of curve on both sides if one side were done first?).
If the inwale is too long, maybe the inner piece tends to stay wetter than the outwale. Or maybe the wood wasn't fully dry originally and the outer section has dried more. Or maybe the two sections just have different properties, as Chip suggests, and the inner section expands more than the outer when both of them get wet.