I'm having a strange problem with my VPS: I can download files from it, I can use PuTTy to connect to it and all behaves normally. But sometimes, when I try to upload a file to the server or save a file via SFTP, the connection inexplicably fails.

I am using jEdit to edit files remotely via SFTP. When it works, it works fine. When it doesn't, I get an error message:

Cannot save: java.io.IOException: inputstream is closed
Cannot save: java.io.IOException: 4:

I can see that a temporary save file (#file.php#save#) is created on the server with a filesize of 0. So the connection works, but when it comes to sending the actual data, something fails.

The same thing with WinSCP, but the error is different:

Copying file fatally failed.
Copying files to remote side failed.

And I can always browse the server with PuTTy without a problem. I see nothing abnormal in any log files. Auth.log shows this when I try to save:

sshd[32638]: Accepted password for - from - port 62272 ssh2
sshd[32638]: pam_unix(sshd:session): session opened for user - by (uid=0)
sshd[32640]: subsystem request for sftp
sshd[32638]: pam_unix(sshd:session): session closed for user -

When I wait for a while (say, an hour), everything works fine again. It can't be a temporary ban, as I am still allowed to connect to the server, right?

I know this may not be enough info to solve the problem, but I am grateful for any clues or bits of information that might help me. What are the possible causes for this kind of behaviour, what log files can I check for clues etc.. I'm running out of ideas!