Nios 2 IDE download verification error

Yes, 5.0 is the first version to verify that the memory contents have been successfully written.

But I need to correct one point. Loading code to a memory which wasn't connected to the data master would never have worked - how could the memory be written by the debugger?

You should debug this by creating an objdump and checking that it matches your memory map. You could also try connecting the debugger without doing a download and trying to write to the memory to ensure it is correctly connected.