James,
The version of PHP Development Tools plugin you are installing to MyEclipse 2016 CI 5 may not be compatible. MyEclipse 2016 CI 5 is based on Eclipse Mars 4.5.1. PDT 4.0.1 is compatible with Eclipse Neon 4.6.0.
Please check this link for the correct update site based on the Eclipse version :
https://wiki.eclipse.org/PDT/Installation
You should use the update site for Eclipse 4.5.1.PDT is a third party tooling in MyEclipse and hence it is not tested as part of MyEclipse. While installing third party plugins to MyEclipse,please ensure the version of the plugin you are installing to MyEclipse is compatible and works as expected in base Eclipse.
Hope this helps. Let us know if you see any issues.
–Swapna
MyEclipse Support