Files are not showed in Finder
I realised that the only volume I was having issues with was a NTFS-formatted volume, for which I use Paragons software to write to the volume. I searched for a solution to my problem and found someone having the same problem:
http://forums.macrumors.com/showthread.php?t=1280829

It turns out Paragon writes the files with read, write flags, AND also the execute flag, which causes the files to not be recognised by the Finder. To solve this, you simply have to put the flags to read and write using chmod 644.

Thanks for all the help!