Epilogue.
Today my sites and test site are all running on the newly released WP 4.0 and all have the latest issue of WordFence running as it should.
I now realise what had happened on my test site yesterday. On this site I keep all the WP themes from Twenty Ten to Twenty Fourteen. During the issue of the WordPress development versions from alpha to beta to RC-1 to RC-3, there were many changes to various files in the WP themes. At the last run WordFence has discovered more than 30 issues (changes to theme files).
This morning all these themes were also updated, together with some plug-ins. After the updates WordFence took the normal time to run because it only found a few issues such as with Akismet, UpdraftPlus and SI-Contact-Form, which have made file changes without changing the version number.