At the final compilation step nLite starts adding everything from second partition.

I haven't done anything unusual, and had to interrrupt nLite, as the compile process was taking forever and over 5GB space.

Tested several times, same story. This is totally nuts.

I can't say for sure, but I'm guessing the only way this could happen is that you somehow managed to include a shortcut into the stuff you wanted to add to your nlite cd.

Seems like it had something to do with an included theme.

[VisualStyles]

Path=D:\Program Files\GUIRelax.msstyles

So it decided to include everything from "D:\Program Files\" for whatever reason.

Weird. At least I figured what the problem was...

It's not weird, themes are usually more than just one file. Also the help on that page says "and their folders". Usually the themes have Shell folders, that's why.