Ok, this may sound obvious to some people but again might not be thought of 
I am noticing alot of people on ICO still have the bugged 1.04 from updating through impulse as 80% of the open games that are not passworded have version conflicts.
It is not me, i bought the retail yesterday and downloaded it through SDC.
Now a possible simple solution.. Why not make a version 1.041 or 1.05 with no difference at all except the version number. This will force all players wanting to play online to update again through SDC (Diasble the impulse update unless you have that fixed now) This will simple just put everyone back in sync as it where, as half the players probably dont visit the forums and don't know about the issue (Noticed alot of players asking why it doesnt work in ICO lobby)
A very simple yet effective way to resolve the issue.
If it is harder than i make it out then disregard me 