Rockstar are advising you not to install the second disk.
http://metro.co.uk/2013/09/16/rockstar-advises-against-full-gta-v-install-download-version-may-be-inferior-4029136/
Absolutely gutted, it came today, but no one to sign for it. I have to go to the sorting office tomorrow morning to get it instead of having it tonight. :shootself