I just stumbled across this thread, wasn't looking for this sour S-04 issue at all... But it made me realize that I too have experienced this! I've only used that yeast twice (rehydrated and fermented in temp controlled chest freezer both times).
The first time was in a double chocolate coffee stout, where I used cold-steeped coffee in the bottling bucket. The beer tasted awesome at first, with a great coffee nose and flavor. But as the coffee mellowed out over time (within the first month or so), I started to notice a sour, almost acidic type flavor coming through. It wasn't too overpowering that I wouldn't not finish the beer or anything, but it definitely made it less tasty than it originally had been. My first though was possible contamination, as I reviewed my process and realized I used an unsanitized coffee grinder to grind the beans before the cold steep. Until I read this thread last night, I assumed that's what it was.
I also have a fresh Pumpkin ESB that I used S-04 in. It bottle carbed up just in time for Halloween last week, and tasted great. I just has another one last night, though, and think that I almost tasted some of that same sour flavor coming out. Was hoping it would get even better by Thanksgiving, but now I'm wondering if it'll just get more sour.
The stout I fermented at 64*F for 12 days, then raised to 68 for 8 days, and then 72 for the last 8 days before bottling (hadn't quite hit expected FG, so raised to try to keep yeast working. S-04 says ideal temp put to 70, but max 75, so I figured it'd be okay...). The ESB I fermented at 60 for 8 days, then raised to 62 for 6 days. Fined with gelatin and crashed at 34 for just one day, then bottled. I aimed for the low end of the range on this one because I didn't want the fruity esters to compete too much with the pumpkin pie spice and pumpkin flavor. I'm hoping the fact of the lower fermentation temps and the gelatin binding more yeast out of the beer will keep this one from getting too sour as well. If I remember, I'll report back in a month or so and update...