ajsiegle,
Sorry that you are seeing this issue.
Can you answer some more questions for us?
1. Can you please share the Installation Details from MyEclipse > Installation Summary > Installation Details ? Paste them here for us.
2. What specifically are you trying to change in the files?
3. Clear the contents of the .log file which is located at <workspace dir>/.metadata/.log. Now replicate the issue and copy paste the contents of the .log file here for us.
4. Could you try removing the javascript builder for the project and see if the error recurs? You can see the builders for the project by right-clicking on the project > Properties > Builders. Uncheck the ‘JavaScript Builder’.
Let us know how it works for you.