This has to do with the .project file and it being ignored by SVN. To see
what I mean, open a terminal window and browse to a PHP project that's
been checked out of SVN. Look at the content of the .project file (cat
project). Now go back to Eclipse and start a new PHP project. Switch back
to the terminal window and look at the .project file for the new project.
See the difference?
Usually, your SVN plugin (I'm using Subversive) will ignore the .project
file so it doesn't get uploaded to your repository when you commit. This
means that if you checkout a PHP project for the first time in your
workspace, the .project file is absent and I guess Eclipse creates one
from scratch. I think it's not smart enough to recognize it as a PHP
project and therefore creates a generic .project file that doesn't connect
to the right PDT plugins. That's my take on it anyway.
I usually manually edit the .project file to the proper format as a
workaround. I keep feeling there has got to be a better way to do it
though...