I'm not completely sure, but I think thunar copies files in the order as they come on the HDD physically and not as they come alphabetically (as it is in the file manager).
Here's an example:
file order on HDD (what you can't see): File1; File5; File3; File6; File2; File4
file order in file manager (what you see): File1; File2; File3; File4; File5; File6
I suspect that thunar follows the "file order on HDD" when copying and not the other one, so this is why your files seem to have a random order (File1; File5; File3; File6; File2; File4) when you copy a whole folder.
Last edited by pusrob; 07-28-2009 at 12:02 PM.