Hi Jon,
As far as I know the loading query or refresh query won't use the clipboard.
And I've tested it on my side, with Clipboard opened. Refresh All did not add anything to the clipboard.
In your case, could you open the clipboard as well, and click on the Clear All button if there are any items there?
Then try refresh your query again, see if that make any difference.
My Excel version is not the exact same one as yours, I will try reproducing the issue you described under the same version and get back to you.
Meanwhile, it's also recommended to usesafe modeto open the Excel, in this way we can rule out the add-ins or Macros in your Excel.
Regards,
Alex Chen