Another tidbit... In FlashFXP use the view raw directory menu option and examine the permissions for the "." folder to see what the perms/owner for root (/) are. Then double check that /Section and . from inside (cwd) /Section are the same and then see if 'site refresh /' or 'site refresh /Section' make any difference if they look different.
If you have a /Sample directory under / in the windows filesystem and you have a mountpoint in your vfs for /Sample to another disk things can get a bit tricky in some rare cases so double check that isn't happening.
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