I got this problem recently when I lost CD 2 of a "post-patch" version of the game. Both versions of this game comes on 2 CDs, but one has been patched.
The item # or version # is printed on the right-hand center of the discs and the "patched" versions have "R01" added onto the end of the number.
I tried to install the game using CD 1 (post-patch) and then stuck in CD 2 (pre-patch) and the installer kicked it out and started asking for the assets3.pk3
file that is not on the pre-patched version. I had to go digging around until I found both CDs of the pre-patched version and install it. Nothing I tried to workaround it was successful.
While I agree that some people might be running into this problem because of a piracy thing, I came looking for a solution to this problem with legitimate copies and couldn't find anything helpful.
This thread was the first one I found mention of it in: