I've never had any shoulder issues with the ol' Pec Deck. I personally find it useful for really hitting the inner pecs hard and helping develop the inner cut down the middle. Dumbbell flyes are great but you can't get your elbows to almost touch like you can on the Pec Deck.
I assume that most of the people who hurt themselves on the Pec Deck tackle it like it's a power exercise when it's more about holding at the peak of the movement and lowering it slowly.
Don't feel bad. Average number of push-ups for the regular joe is something like 24.
I was wondering why you hadn't posted in this thread in a while. I was worried that you'd gone fatty on us again. Glad to see you're back in action.
The gf and I are planning a trip to Philly in the next few weeks. Maybe we can meet up while we're there if you promise not to grow tentacles and rape her or anything.

