korell: So, for the retail discs to be affected then the wrong version game files would need to be on them too
bansama: Nope. You're forgetting that Steam will compare the files installed to those it thinks are the most uptodate ones. Thus, in that case, you're more likely to be forced to download the wrong files (and, worst case, the entire game).
For that matter, retail versions of Steamworks games don't always carry all the files anyhow, which is why there's often complaints from people having to download a portion of the game. (It's even worse when there are day zero patches...)
Yes, you are right, forgot about how Steam would look at the files that the retail discs installs and would detect them as the incorrect version thus forcing a download from Steam to replace them. >_<
Anyway, my copy has just been dispatched by Amazon so hopefully this whole issue is now resolved and won't affect me when I get to install it.
I think the missing files from retail copies are there to force some kind of Steam DRM protection to prevent full copies from getting 'out there' unless it has been verified by Steam. Sometimes, though, the retail installer and Steam don't get along well and it tries to download the full game from Steam anyway (as was the case with Duke Nukem Forever for many people) but there are ways to force Steam to use the disc to install.