Hmmm… I'm not 100% sure I know what's going on. What does your alpha actually look like? A black landmass on white? White on black? A thin white outline? I don't work with Gimp, so I can't really give any direct advice, but if we can clarify your question before one of the Gimp users comes along, we'll get you to a solution faster.

I suspect that Gimp is treating the alpha like a real alpha. Every program out there other than Photoshop takes "alpha" to mean "transparency." While storing saved selections in the channel box means you can do some cool stuff, it's a little bit bewildering since you don't often use those "alphas" as real channels. Consequently, when you have a four-channel image, if you haven't explicitly told Photoshop to use one of them as transparency, it can be surprising when another piece of software treats it that way anyway.