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I have found that dreamweaver and notepad++ suffer from the same problem. They add hidden characters that cause scripts to not run properly on some OS's. Character encoding is a serious issue when dealing with *nix OS flavors. With that in mind I either use geany (for quick edits) or NetBeans (7 beta) for projects.
I also noted an odd issue when I was using notepad++ and the explorer plugin... for some reason, on occasion, it would somehow corrupt the security descriptors of my windows partitions. It would lock up and the next thing you know I was having partition issues. I am still not sure what exactly the issue was but I stopped using it and haven't had any more issues with partition corruption.
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