I have the same issue. I have contacted Evernote Support and they took note of the issue. But they have no timeline for this resolce.
They completely give up on the clipper which works terribly. Beside the issue with the order, it also doesn't work for me when the app is closed (clipping will disappear after I press Save to Evernote) and the keyboard shortcut won't work unless I open the clipper menu once. Loosy.
Evernote won't care much about their paying consumers. Now their priority are B2B users.