Make sure you have the latest videocard drivers installed. If you don't, I've seen some computers without them, not display any sort of shaders in these types of games.

Also like Dynasoft said, Make sure you're in a Direct3D mode. Not DirectX or Standard.

And make sure your graphics card feature the pixelshader version required.

Dynasoft was right, they all work now, except AND/OR/XOR. These three do work in my normal version of MMF2. Any ideas?

AND/OR/XOR don't work in HWA, because they work on the bits in a colour represented as an integer (0 to 255 per colour channel), and HWA works with full floating-point colours (0.0 to 1.0 per colour channel, in theory can even go outside that).

Oh ok I see. That kind of sucks. Thanks.

The effects can be replicated with shaders though.

e.g. for lights you can replace "and" with "multiply". "or" is better replaced with "add".

You can have a layer in front of everything filled with lights (any colours!) set to "add", and then set the whole layer to multiply. Should give a VERY nice lighting system.