Awesome job on this. Thanks for taking the time to make it. Looking forward to see how it evolves. It's fun to play in 3d. But also hard on the eyes after a while (though I don't blame your mod, it seems to be the nature of 3d stuff. Especially this more primitive color based system).
STOP! If you read the post I briefly had posted here, don't do it! I forgot that I changed Anaglyph from a boolean to int. Manyaglyph is currently NOT compatible with Modloader. I will investigate the necessary steps for me to make it compatible. For now, do NOT attempt to use them both!
Are you sure you don't have red-green (red is on the left when wearing) glasses? Red-greens should work fine with red-cyan mode, there aren't really any optimizations that can be made for that specific combination.
iverie: Hmm. Perhaps it would be easier if we knew what operating system you were using. Are you playing in the browser or using the launcher? As far as I know, it won't work in the browser, you have to use the launcher. Another Also, have you tried deleting the bin folder and redownloading minecraft, then reinstalling the mod?
At the moment the only way to change the colors is by editing the source code. However, I've thought about adding a mode that loads it from an external text file, I'll look into it somewhere along the line.