Copying large files under Windows 8.1, from one NTFS filesystem to another NTFS filesystem, results in only the first 4 GiB copied and the rest of the file is ignored.
So, if you think to have files larger than 4 GiB, instead of doing:
copy($source,$destination);
it is much better to do something like:
exec("xcopy $source $destination");
I will check to see if this issue is valid also under Linux.
It depends on PHP not being compiled in 64 bit mode?