This sounds rather similar to an old PHP bug (#25482).
I wouldn't think any setting in your .ini file would affect the lint check mode of PHP, however as a test have you tried renaming or moving your .ini file (meaning PHP won't be able to find it and should revert to the built-in default values for all directives)? Do you have any other Zend software installed?
Also, which package did you use to install PHP, the .zip or the .msi download?
EDIT: Also, thread moved to Install forum (this seems more like a compilation/installation error rather than one caused by the Windows OS itself).