Why can't I modify files on ubuntu when I am connecting with

I'm using the latest version and on Windows 7 via SFTP protocol

I've tried different ways and read some solutions including these:

• Why I am not able to ssh as root?
  
• https://serverfault.com/questions/196527/editing-with-winscp
  
• Ubuntu Forums
  

I don't understand why when I connect with ubuntu via PuTTY, I can have root permission and modify files. However, when I connect with ubuntu via WinSCP, I'm another user(I used the same username and same private key(pem) on both connecting software) and can't modify files.

Then I found some possible solutions from the links above. I tried to set root password and PermitRootLogin. But then, when I log in with the root username, it says the file is too big, whereas when I changed the username back to ubuntu, then it works(file is size has no problem, but I can't modify files when I'm not root user).

I am very confused, please anybody if you can point me out, I'd be much appreciated.

Your duplicate question (with my answer) on serverfault.com:
Getting "Received too large SFTP packet" error when connecting with root account to the server via WinSCP