Steps to replicate:

1) Create a dynamic web project TestProject
2) Create a server
3) Add/Remove action in servers view. You will see the module name is TestProject
4) Open the component.xml file in .settings folder and change deploy-name to some new value (RobsTest)
5) Add/Remove, note module name didn't change
6) Publish deployment, note its still deploying as TestProject
7) Close project, then re-open it
8) Add/Remove action, note the module now reads TestProject (RobsTest) (or similar)
9) Publish, note module is deployed as RobsTest.war