I have a similar problem. I bought the Original Sword of the Stars, then BoB, then AMOC as boxed games. Installed fine. Now that ANY is out, I bought it from Impulse in June 2009 since that is now my preferred download source.
It downloaded OK, although it went to the C:\ root since I forgot to tell it where the original install was. But no problem, I just copied the files into the correct directory, put in my email and serial when it asked me and everything was just fine until a couple of days ago (Feb 2010).
I discovered that there was a patch taking it from v171 to v172, with some very important bug fixes. Problem is, Impulse won't update the install. I went into the blue corner box and told it the correct path, and it duly downloaded some files. They were the 171 files not the 172 ones! Worse still, having done this it now asks for the CD before playing? What CD? ANY was a download, not a CD. Does it want the AMOC, BoB or original CD?
No matter what I do, Impulse will not download the 172 version. Please help...