透明GIFがうまくゆきません...

This is usually due to a browser bug. Make them non-transparent or accept that a particular browser will not display them very well. In particular, some browsers do not display transparent GIFs well in 16-color modes under Windows. You may also wish to respectfully suggest to users of 16-color Windows that they try switching to a 256-color mode. Most graphics cards support 256 colors, but a surprising number of machines are configured for 16 colors instead.
World Wide Web FAQ 1