I had a similar problem before with eclipse (either CFEclipse or Bolt beta - can't remember now). I think the fix was to create a new workspace. Just go to "File > Switch Workspace" and create a new one. Maybe give that a try and report back.
I have two things to report:
1. I was impatient and tried the uninstall and install. This actually hosed all my editors. After the uninstall and reinstall of ColdFusion builder, all of my editors gave the same kind of message that the CF Builder gave on the cfm files.
2. I switched workspaces and that got rid of the message but none of my editors are recognized any more. All files open as just text.
I am not going to try to debug this. I am going to start over with eclipse and all my subsequent plug in installs. So lame.
After moving my old Eclipse install, I created a new one with all my favorite plug-ins (Aptana, CFBuilder, SQLExplorer, Subclipse) and then pointed my workspace at my previous workspace. Everything worked fine. So, this tells me that my workspace was not mangled but the issue was really in the Eclipse install folder as caused by the CFBuilder updater.
After running the updater you should start ecipse with -clean option from command promt as >eclipse -clean .
Have you done this?