Whenever you delete a Java project, it's launch configuration ( File > Export > (type) > Launch Configuration ) remains on the list ( and is invalid ).
The invalid configuration does not show up on Run > Run Configurations ( after the project is deleted ), and there is no way to delete them from inside of Eclipse.
The problem with this bug is that every time you go to export a project, you have to pick a launch configuration from a list containing both valid and invalid options.
The more dead projects there are, the harder it is to find the correct launch configuration. In my case, I had 66 Launch Configurations, with only 6 of them being valid.
To fix the problem, you can delete the invalid configs by hand. They are located in the following file
(Wherever Eclipse Saves It's Files At) \.metadata\.plugins\org.eclipse.debug.core\.launches