Is locale setting same for both your Windows system and Linux server?
Can you once try to open any of those directories in this way:-
Just type first 1 or 2 or 3 characters of a directory name and hit tab
key from the keyboard. Linux shell will then automatically insert bachslashes (\)
before any special characters in dir. name.
~$ cd sam[tab]
Second, if any file/dir. name has some special or unrecognized characters, then you can put the file/dir. name in double-quotes like:
~$ cd "s@mple file"
Although this is just based on my experience, but you can try it. If it don't help, then share some file/name as it's showing in Linux.