Hi,
This is probably a 'feature' operating as designed, just checking. Recently I changed the WF options on a couple of sites to also scan plugin files (previously I had this turned off). Now whenever I get the message that a plugin needs an upgrade, I also get a couple of warnings about modified plugin files. Which is only logic, as WF compares the plugin files against their newest version. Still this is somewhat confusing, as I am always extra alerted when I see a message about a modified file. For me file comparison and warnings about modifications of WP core and plugin files is the most useful feature of WF, because as long as there are no such warnings, chances are low there's a contamination, hack, virus or whatever wrong.
I would prefer WF compared the plugin files against the version I am currently running, even if this is not the newest. However, I can imagine this may not be possible. Is it?
Erik
WP Webbouw