Update: I've actually found a solution.
You said you used a Mac to copy the files, right? Just so happens I did too, and I suffered the same bug.
The same problem actually caused crashes in Yet Another Wad Manager Mod on vWii.
Let me walk you through the solution. (Note: I am not responsible for file loss through typos of these commands.)
Step 1: Insert your SD Card into your Mac.
Step 2: Open the Terminal Program (via Launchpad, Fn+F4 keys)
Step 3: Type "sudo find " with the following spacebar, but DON'T PRESS ENTER YET!
Step 4: Drag+Drop your SD Card from your desktop into the Terminal window. Once again, don't press enter yet.
Step 5: After the path for your SD Card, type "-name '._*' -type f" The full command should look like this:
sudo find /Volumes/<SD Card> -name '._*' -type f
Step 6: Now press enter. Type your password when asked by the system. How many files showed up in the list? Did they all have "._" at the beginning of the name? These files are the source of your problems.
Step 7: Press the up arrow key, you will notice that the previous command has been re-typed. Don't press enter yet.
Step 8: To the end of the previous command, type " -detete". The full command should look like this:
sudo find /Volumes/<SD Card> -name '._*' -type f -delete
Step 9: Now press enter. Once the process completes, type 'logout' into the terminal and press enter. Now close the terminal and eject your SD Card.
Step 10: Enjoy your homebrew.
If the problem ever resurfaces, just run these terminal commands again.