I'd look at the project properties (Right click on the project, last menu item), at the Builders tab: there should be a Validation and a Script builder added (at least I have those two in Eclipse 3.6, and the Script builder is required for PHP). If they are missing, there is a chance, that the project lost its PHP nature.
If the nature is missing, look for the .project file in the root folder of the project (it is by default hidden, but you could either show .* files, or view it in the File navigator outside Eclipse. At the end of file, there should the PHP nature be added:
<natures>
<nature>org.eclipse.php.core.PHPNature</nature>
</natures>
If the nature and builders are set correctly, I don't know, what might have caused your problem.
Update: the relevant part of my .project file looks as following: try to update yours.
<buildSpec>
<buildCommand>
<name>org.eclipse.wst.validation.validationbuilder</name>
<arguments>
</arguments>
</buildCommand>
<buildCommand>
<name>org.eclipse.dltk.core.scriptbuilder</name>
<arguments>
</arguments>
</buildCommand>
</buildSpec>
<natures>
<nature>org.eclipse.php.core.PHPNature</nature>
</natures>