This is a known issue when using Evernote on Snagit for Mac 3 and earlier.
Snagit on Mac 4
To use Evernote with Snagit on Mac 4, please use it via the Mac OS X extension. For more information about Mac OS X extensions and Snagit, please see here.
Snagit on Mac 3
Currently, the best workaround is to either save the image and manually upload to Evernote, or to download and install the Evernote App, and Share to the Evernote application from Snagit. To do this, once the Evernote App is installed, open Snagit and navigate to the file menu Snagit > Preferences > Outputs > Evernote. Change this from Share to Evernote on the web to Share to Evernote application.