I don’t have either Cubase version, but I can make a suggestion. I attempt to solve most problems by Process of Elimination.
It may be a problem with only one WAV file. With the Cubase 5 files on the flash drive and working, copy/replace only one file at a time, testing them on the mixer each time between file copies.
If you are certain that all parameters are set the same in both versions, then perhaps a file-compare utility/app can find what is different between flash drive copies.
Sorry I couldn’t help more. Just giving you food for thought. Good luck.