I don’t know why handbrake would not produce a compatible file but, as mentioned above, try Davinci Resolve (but I think you need Windows 10 for this). It’s more difficult to use than a simple conversion utility, but Cubase will be more likely to be able to read the file if you save it in a standard format in Resolve.
Anyway, I’ve just noticed it looks like you’re on Windows 7… so you can’t use Resolve anyway. 
Maybe there’s another Win 7 conversion utility out there that will do the job.