I am in the same situation.
It seems that Apple has updated Keynote (version 6) and it does not support opening presentations created in older versions. This is true on the iPad and appears to be the case on the desktop. I can not open a single presentation that I had done in version 5. The version 6 of Keynote has been fraught with mistakes and I have since quit using it for presentations on the iPad.
Since there are other issues with the loss of tools and a decent GUI in Keynote, Apple really messed this application up to the point where I will not rely upon this again.
As much as I detest Prezi's pricing and policies, they may be the best way to go at this point since there is no problem with opening older presentations therein.