It sounds like you may have mre than one version of Numbers installed on your Mac. and that the older one is attempting to open these files.
If you were previously using Numbers '09, and upgraded to Numbers 3, the older version will still be on the Mac, enclosed in a folder named iWork '09, found in your Applications folder.
Numbers 3 will also be in the Applications folder, but not enclosed in another folder.
The two versions have different feature sets, and I would caution against removing the earlier version before ensuring that any features you have been using and that you need are supported in Numbers 3. Both versions can coexist on the same machine (and according to reports, can both be running at the same time).
To ensure that you are launching the newer version, make sure you have it's icon on the Dock, and that you use that icon to start the launch. The icons for the two versions are similar—both are vertical bar graphs in 3D format. The difference is in the number of bars—three for Numbers '09 and four for Numbers 3. Once you ahve launched the needed version, use File > Open (or File > Recent items) to locte and open the file.