First, if you're on a mac you're going to need to show hidden files. Open up terminal and type the following:
defaults write com.apple.Finder AppleShowAllFiles YES
Restart Finder
KillAll Finder
Now that you can view hidden files, navigate to your default workspace. Mine is set for /Users/joeholst/Sites but you may have set your default workspace to be somewhere else.
Once you locate your default workspace drill down into the file noted below:
.metadata\.plugins\org.eclipse.core.runtime\.settings\org.cfeclipse.cfml.prefs
Once you locate that file, open it up and add a new line with the following text:
lineNumberRuler=true
You'll probably need to restart Eclipse for the changes to take effect. This first happened to me when I upgraded to Ganymede. I downgraded back to Eclipse 3.3 and the problem was still there. Anyway this should get you taken care of.
By the way, to restore your finder hidden files back to the way they were just run the command and put AppleShowAllFiles NO.
defaults write com.apple.Finder AppleShowAllFiles NO
I haven't verified but am guessing the solution is similar for windows users, I'm not aware that the problem even exists for windows users though.
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I came across this issue and I am using XP so it does look like it affects windows too. I'm using Europa 3.3.2 and cfeclipse 1.3.2.beta
Thanks again