Are you just counting North American box office then? Cloud Atlas broke even if you're counting worldwide BO. In any case, I wouldn't describe that as a clear flop. (Especially with piecemeal funding and home video.) More like a flatline. Same with Ninja Assassin.
Speed Racer was a definite flop.
The film studios don't get 100% of the box office. Cinemas take a cut etc. It varies on movie, how long since release, country etc. However when all is said and done generally saying around 50% is a rough estimate. Looking at Cloud Atlas it seems the budget was 102m and it took in 130m worldwide.
Usually the budget is just production not marketing. However even if that was production + marketing it would still be a budget of 102m for a return of 65m. Definitely a flop. Likely broke even eventually with dvds, tv etc.
For me I think most likely Jupiter Ascending. It just seems like a tricky one to market.
I don't think GotG will bomb however I'm a little concerned it will underperform. Hopefully that's not the case. However it's definitely a different tone of superhero movie.