Thanks very much for the suggestions. I quickly narrowed the issue down to the Compare plugin. When just the Compare plugin is installed, when I hit "compare" for two files, I noted that typically one of them will be partially converted to plain b&w text, and then when I hit "clear results" after a compare, it changes both the files to entirely plain b&w text, and I can only get back the proper format temporarily as described above. Without the Compare plugin and with my other plugins installed, no issues. Changing the extensions to .js has no impact on any of the above.
I do use the Compare plugin heavily, however, so it would be great if someone could repeat some or all of my experience to confirm this.
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