Here is the complete list of steps to work around this problem:
1) From Eclipse, create a new PHP project, including a new PHP file within
it.
2) From a terminal, copy the .project file from the newly created project
to all checked-out projects. Manually edit the copied .project files to
reflect the proper project name (between the <name></name> tags).
3) Copy the .buildpath file from the newly created project to all
checked-out ones. Manually edit the copied .buildpath files to reflect
your environment (I don't use this personally so you'll have to figure it
out).
4) Copy the .settings/ folder from the newly created project to all
checked-out ones. In the folder is a file named
org.eclipse.php.core.prefs. Manually edit this file for all checked-out
projects to reflect the proper project include path (after the
include_path= make sure you have 0;<your include paths separated by
semi-colons> so it looks like this: include_path=0;<your path 1>;<your
path 2> )
5) Restart Eclipse.
Hope that helps. Hope also that someone would tell me a better way to do
this...