This problem occurs when the plugin requires a variable. For this example let's use the phonegap-plugin-push plugin but you can reproduce this with any plugin requiring a variable.
Click on add plugin
Click on third party plugin
Click on local
Browse to the plugin and select it.
(Don't add the variable/value yet... )
XDK will come back and ask you for the value for the missing variable (in this case XDK knows that SENDER_ID is required and prompts you to enter the value for SENDER_ID).
Enter the required value and click OK.
Wash, rinse, repeat until you're tired of trying.
Obviously, the workaround is to enter the variable by name/value before adding the plugin.