I’m unconvinced that this can be attributed entirely to Eclipse 3.3.0. I’ve been running Eclipse 3.3.0 on my SuSE Linux box since the introduction of MyEclipse 6.0.0. I did NOT see this font problem with that combination. I’ve only seen this issue since upgrading to MyEclipse to 6.0.1. That tells me it’s something MyEclipse is doing.
Also, although I see this problem with JSEclipse, I also see it editing simple text files (Linux shell scripts, Windows batch files, …) and XML files. This isn’t an issue just with JSEclipse. I find it most ANNOYING with JSEclipse as I spent a great deal of time editing JavaScript with it. I’ve gotten in the habit of shutting down Eclipse with a JavaScript file open so that the next time I start it, it starts with a JavaScript file with a fixed pitch font. Problem is if I then have to edit an XML file or shell script that I have to open it and go through the font fixup process described in an earlier post.