Wildcat and Dark Man X, yes, I believe the start menu can only be transparent on Windows 2000. This is because 2000 is Windows 5.0/NT kernel, and 95/98/ME are the Windows 4.0/9X kernel. The NT kernel includes better API's for things like alpha-blending and transparency.
On 9X, WindowFX actually does not make anything *really* transparent. It takes a picture of whatever is going to be under the menu, and interlaces that picture onto the background of the menu. And since the Start Menu is, according to Windows, not technically a real menu, WFX does not do it's job when Start menu is open, because it doesn't realize that it's a menu.
On Win2000, the Start Menu is treated much more like a standard menu. And WFX uses W2K's inherent API's for the alpha-blending so the menus are truly transparent.
I'm sure that was way more of an answer than you were interested in knowing, but that's why.
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---Skorpion