Hi Mark,
I had due to making changes to one of the theme PHP files and there was an indication of a change on a readme file from plugin long time ago (although it looked fine, just a line removed of text removed and version number changed when I compared changes).
I "unignored" the plugin readme file I had set using "ignore until file changes" and ran a scan again. Same thing occurred saying:
Comparing open source themes and comparing plugins WordPress.org originals highlighted red with "Problems found."
But on scan completing it returning no issues.
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On another website I have the Wordfence plugin on I just selected "ignore until file changes" on a php file I had edited. I ran a scan again and this time it also now shows:
Comparing open source themes against WordPress.org originals - Problems found.
Now looking like if you select "choose to ignore until file changes" it is still registering it as a problem, but it's not if you know what I mean :).
Might be something to do with latest version, worked fine previously