As a portable app user I sometimes keep several versions of the same program on my flash drive. That is usually not an issue as the different versions are in different folders.
Seems that Codysafe does not care about folder names (sort of), if the program has the same file name for different versions only the last one setup in Codysafe will actually show up. You must rename the exe files to work around this issue.
Hopefully that will be fixed in the future.
Other than that a good program so far.