I may have had the same issue. My DVD had many zero-byte long files -- and those were the ones that came up with a message indicating the file was not found. (Click "Ignore" when prompted to Retry/Ignore/Cancel and it'll skip the file, until it finds another zero-byte sized file).
I copied the entire folders and files over to a folder on my hard disk, then ran the installation from the hard disk (ran setup.exe). Copying to HD appears to avoid the error messages about those zero-byte sized files not being found.
After running the setup, and since I previously have used stardock software before, I ran Stardock Central, manually entered the DVD key code from inside the game case to my Stardock account, and once registered, ran the game update from within Stardock Central. It appears to have managed to figure out which files were in need of fixing because so far the game runs. If you don't have Stardock Central, I believe it's a free download from stardock.com. It took a while, but I didn't had to go back to the store for a disk replacement... though I'm not convinced it's a 'bad' DVD, because several posts recently speak of similar/same problems. Maybe a batch of DVDs weren't burned correctly.
Stardock Forums
Sins Forums