Do not use the notebook when you change the php script directly on the web.
I used the notebook when I changed my jcow, but it did not work all that I made and the changes were wrong.

I switched over to an ftp program called Web Ceo is a free program. When did all of my script, easy to use too.

I have used notepad quite a few times without any problems.
I was using filezilla FTP, maybe you uploaded in the wrong format/setting on the FTP client?

I'm using Notepad ++ now and have never had any problems.