Synergy & Automator

This might be for one of two reasons:

• Synergy is a faceless background application (so it won't appear in the Dock, in the application switcher HUD etc), and this might be why you can't add it
• The faceless background app, Synergy.app, is actually bundled inside something else (in 3.2 it's inside Synergy.prefPane/Contents/Resources/ and in 3.5 it's inside Synergy Preferences.app/Contents/Resources/Synergy.prefPane/Contents/Resources/

Depending on how you actually select items to be added to your exception list, it could be either of those two reasons. Does the script provide you with a list of candidates based on what's currently running? Or does it provide you with a standard file chooser and you're supposed to navigate and choose the application to exclude?

If it's the latter case you might be able to make things work like this:

1. Navigate to where you have Synergy installed in the Finder; right-click or control-click on the package and choose "Show package contents" from the contextual menu: in this way you'll be able to "drill down" and actually expose the Synergy.app itself
2. Now in your Automator script setup, when the file dialog appears, switch back to the Finder and then drag Synergy.app back onto the dialog; it might let you select it that way

But this is all speculation on my part: I've barely used Automator myself. If this doesn't help, send me a copy of your Automator script if you can and I'll take a look at it.