Having the same problem with Safari Version 14.0 (15610.1.28.1.9, 15610) with macOS Catalina Version 10.15.6.
It really is something that I've been experiencing for the last couple of years. The difference now, with the upgrade to Safari 14, is that the Clipper doesn't alway function after the refresh. Sometimes, multiple clicks achieves the proper response, where a single click does nothing. This is becoming more and more unusable.
I've been using Evernote since the very beginning. It looks like I will have to avoid the Clipper and go back the "Control-Command-V" capture option instead. This is functionally problematic since, you don't get the header and the web link information to populate; it has to be entered manually.
Not good and getting to be completely unsatisfactory!