I don't know about GPT or MBR affecting it... but i know that file system is not the only issue...
there is file system, OS, the file copy program used (the OS's built in one, or a custom one used in certain tools, like backup programs, then there are sometimes different systems for different actions, such as copying over a network)...
so anyways, its not just a matter of FS.
You know, I am curious to know if NTFS compression could affect it as well, I never heard of it making a difference, but knowing how it works I theorize that it would... Anyone knows?
PS. just an FYI, the "filename too long" error means that filename + directory names are too long... the full filename is something such as:
C:\Games\Data\Saves\Blah blah blah.sav
So if you copy a file from "C:\Games" to "C:\Mybackups\Taltamirs backups\games" you might have this error purely because the directory and subdirectories total length is longer. This was an issue for me which is why I always backup to a shorter named folder than the original folder.
PS. seriously, why is there no "do not parse emoticons" checkbox anymore? there used to be one and it essential!