In flash, did you use the background color as your white in the hands? It should become transparent after export. Take the bucket and fill the hands with white color to ensure they stay that way. Alternative: Pick a slightly more grey color for the hands if first approach doesn't work.
Well, you could edit the alpha channel like Chrilley said. In this case, the hand and the border are connected, so it should be fine to just color in the hand with white while editing the alpha channel (see his post). In some cases though, that can leave artifacts if you're not super careful.
You could convert the alpha channel to plain old transparency, but since you drew it in flash I'd imagine the edges are anti-aliased and would look funky if you did that.
You ought to download GIMP if you don't have it anyway, so open the PNG with that or photoshop and do your tweaking before saving it again. In GIMP you have greater control over what's transparent and what is colored in. If I recall, flash just has a white background, so it's hard to tell what's transparent and what's white.
From my expirience, Flash is terrible with everything except Flash, but that's probably because I haven't played with it too much. After Effects is 10x better for character animation, in my opinion, especially if you're only using Flash for it's movement and animation tools (which is what After Effects is better at). Flash did a good job of putting together animation tools, programming and vector art into a nice little package, but unfortunatly doesn't do any as well as art in Photoshop, animation in After Effects and Vector art in Illustrator. But be forwarned with using After Effects, the title says it all, "AFTER" effects, which implies that you should make your assets in another program first. You can, however, do things within After Effects, it's all up to what kind of style you're going for. If you happen to have a copy or can pick up one, I am definatly more than willing to show you some awesome techniques that will take hours of work out of animation.
In terms of MMF2s importing, I think that just might be what everyone said with the alpha channel importing. I've played around with this quite a bit. When you're using PNG's, it's best to either put it into RGB color mode or Indexed color mode. Indexed color mode restricts the palette to 256 colors, and does not have an alpha channel, so the easy fix for that is to make the background a color like magenta or something that isn't used anywhere else in your image. If you leave it in RGB color mode (which I assume is what is going on), you just have to make sure the alpha channel is spot on (which I have no idea how to do in Flash, I simply just had too many issues with it to continue messing around with it). If you have a copy of Photoshop, or GIMP, it's probably best to run it through that to make sure it's good.
Photoshop is really nice because of the actions and batch processes. Usually when I do animations, I'm left with tons different images as frames, with the actions, I just go through and do one of the images that I want to edit (litterally anything from color changes, to filling in the background, or changing the color mode), then plug that action into the batch command and tell it the folder of all my images, and presto, it'll do the same thing to all of them, saving me from doing them each individually (and if you've got even 20 images, doing them one by one is a pain in the ass).
And in terms of maximizing your importing into MMF2, the best advice I can give is to load all your frames into the stopped animation, and control the frames that it plays through code, so that way, any time you make changes to your frames (especially if you export them all as a PNG image sequence from Flash or After Effects), you don't have to keep futzing around with placing them neatly into each animation, the code is already finished for you. That and remember that Alt+Clicking on Crop and Shift+Changing the Action Point/Hot Spot will do the same for all of your frames.
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