I came across a similar issue and found a fix for it, however, it's a bit of hack as I couldn't find a way to make the change in the Eclipse Menus. Basically I needed to add the following .buildpath file to the root of the project folder:
<?xml version="1.0" encoding="UTF-8"?>
<buildpath>
<buildpathentry kind="src" path=""/>
<buildpathentry kind="con" path="org.eclipse.php.core.LANGUAGE"/>
</buildpath>
If you already have a .buildpath file you could probably just add the line to the existing file:
<buildpathentry kind="con" path="org.eclipse.php.core.LANGUAGE"/>
I believe I came across this issue when I created a project from existing source instead of creating a new project.
Its been a month since you asked your question so hopefully this is still helpful.