Blockchain.info really does not use software in a sense that people have a choice which version they use (or even have any idea what version they are using). The majority (probably 99%+) of their users access their wallet service via their website and could really only use an "old" version if they are running it from the cashe in their browser.
In theory he could have used their software from github and host it locally, but I would kind of doubt he was doing this
They have an iOS app, an Android App, and a Chrome Plug-in in addition to their website.
If the website was used, then the fee would have been included. Therefore, it seems clear that he was using one of their other other clients.