First, this really belongs in the questions sub-forum. =).
Second, there's sort of 2 parts to getting native res during the boot process. First there's within Cham UI, then there's the apple grey loading screen. For the latter, setting it in boot.plist is the way to do it, whether you do it using Lizard app or manually. To set the resolution within the Cham UI, well it depends on the version of Chameleon. If you have a very early version of RC5 or RC4 or less, you'll want to set it within the plist of the theme folder itself. For newer RC5 builds, you don't have to do anything, as it reads the resolution from the same apple.boot.plist from above.
For BOTH of these to work, the graphics card itself needs to support the resolution you want as a VESA standard. This is independent of the OS and does not use any card specific drivers. If it doesn't support the res via VESA then neither will work at all. This may be what is happening here. Have you tried going into graphics info within ChamUI options? Does it list the resolution you want there? If that doesn't get you started on the problem, then you may want to check out: http://forum.voodooprojects.org/index.php/topic,1181.0.html
Regarding the apple grey screen, I'm not sure I understand, you want to get rid of the entire loading section of the bootup process? If you mean the color of the background, then no, you cannot change it, at least not technically. Cham allows you to change the apple icon it uses, you could swap out that image, with an image that is the entire size of the screen resolution, allowing you to have what ever background you'd like. The image is boot.png within the theme folder.