Hmm. Basically it wasn't as easy as I thought. The GIF decoder built into all Pocket PCs (IMGDECMP.DLL) does not in itself decode GIFs correctly.
The way IMGDECMP works now is so that all transparent parts of a GIF image are rendered with a white color (regardless if you ask it to specifically use another color). When Pocket Internet Explorer draws a transparent GIF it simply replaces all these white pixels in the transparent GIF (including the mask background which has become white during the rendering process) with the background image.
This has the effect that if you have white pixels in your GIF image they will simply be replaced by the background. I have attached a picture below illustrating how this looks like in Internet Explorer:
So, the solution to your problem is either:
(1) You could try and set the color key to RGB(255, 255, 255) and hope that you don't have any white pixels in your transparent GIFs. This way they will load correctly with GapiDraw 1.03 without having to modify them
(2) Batch convert all images into another format.
By the way.. You are aware that a license is required if you want to use GIF images in your product? It is very simple to scan your file for GIF images, and it is currently done by robots on the Internet. I would strongly suggest that noone uses GIF images for anything really, both due to the patent and now also since the GIF decoder in all Pocket PCs are corrupt.