I'm guessing that you have IPython 0.12?
The notebooks without v2
are probably format version 3, which was introduced with IPython 0.13. 0.12 can't read format v3. The reason that the tarball has both is to allow for IPython 0.12 users, so you can just use those.
If you want to upgrade, the IPython PPA has the latest stable version. Be aware that this will update your notebooks to format v3 next time you save them.