Plugabugz: This is typical comic book logic. Events in single series comics rarely have effects on the main universe unless a crossover event is going on. Think about it...there is no way a different writing teams in comics can come together and make sure every series references and draws story ideas from each other perfectly.
So in the same way the stories in the ongoing TV series only reference each other when a crossover event is going on. You should be thankful actually, because it means you can just enjoy one series at a time.
Personally, if I every managed DC or Marvel, I would either A) Scrape every individual comic series and just make a singular DC universe series which would be 2-3 comics a week that could tell a story using any characters, but then I would chart out a 1/4 of a years stories at the same time and make sure all the writers relate to each other.
If that couldn't easily work, I would isolate the stories, but then have one DC universe comic that told big stories references all the characters working together. Imagine if CW didn't have 4 different series of television, but had one DC universe series that aired every day, and could use ALL the characters (but didn't have to.) That would be perfect.