Wibbly wobbly, timey wimey bits :) remember that River's timeline isn't exactly in sync with the Doctor's and the series :)
It IS possible that she used a different vortex manipulator, or other time travel device. She IS a bit of a timelady :)
It's highly likely that she bought a vortex manipulator from Dorium in "The Pandorica Opens" precisely because she was familiar with the things, having used them in the past (i.e., her past).
It's also possible that she did, in fact, use the vortex manipulator she'll buy from Dorium in her future. In "The Pandorica Opens"/"The Big Bang", she gave it to the Doctor. He used it to take the Pandorica into the TARDIS explosion. If it survived, as he did, and ended up in the TARDIS, as he did, it would have been brought back by Amy, along with the TARDIS and the Doctor. The Doctor would still have the thing and be able to give it to River at an earlier point in her timestream. As the first responder said: "Wibbly wobbly, timey wimey."
Actually, River uses the Vortex Manipulator at the end of "The Big Bang" after telling the Doctor he will soon find out who she is. She also uses it at the end of "The Wedding of River Song" after the events of "Flesh and Stone" to see Amy. She also used in "The Angels Take Manhattan", and that is the last time we see her with it.