I have had this same problem. I bought season 2 on PS3 disc, and every time I try a play through I have this problem. Also, I cannot get the prompt to download the patch to appear. Yes, before you ask I am signed in to psn. My region is Canada, if that matters.
The Season Two disc version does not have an update/patch to download, and all content is included on the disc. Can you please clarify where you are experiencing the issue in the game? What episode are you experiencing this in? Can you please clarify if you can still access your saves by going to the Save Files menu from the main menu of the game?
The first play through, it happened near the end of episode 4. The second, was near the third episode. I was unable to retrieve my season 2 save either time and had to restart from the beginning. Season 1 saves do not appear to be affected.
I apologize for the inconvenience. We have had a few reports from players experiencing this issue, and are currently looking further into the root cause of the issue. We hope to have a resolution in the near future. Unfortunately at this time, the only workaround is to upload your saves to the Playstation Online Storage and start a new game, or delete the Save Data Utility for the game from the Save Data Utility menu on your PS3's XMB, and start a new game in Season Two. Again, my apologies for any difficulties this may cause you, as we look further into the issue.