Rather than start a new thread, I found this one describing my problem exactly. I hope I behaved correctly.
I created site, I created FTP user and uploaded files, I created shell user and after editing and saving a file (using vi), I was greeted with:
E138: Can't write viminfo file /var/www/clients/client0/web3/.viminfo!
The file is in fact saved as edited, but I get the error message.
So I searched and found this thread. After logging off, enabling jailkit for the shell user in ISPCONFIG interface, and then logging in again, I see nothing when performing "ls". Therefore, I disable jailkit for the user, and after logging in again the user can see and edit the files again, but again with the error message.
What does this mean? Can I "fix" things so the shell user doesn't get this warning?