On case-insensitive filesystems (such as the default HFS+ configuration on Mac), scisr.php and Scisr.php conflict and only one of the files is saved to disk when Scisr is checked out from git or unpacked from a tarball. I think the ideal solution is to rename "scisr.php" to "scisr" as it is an executable script with a #! line. It does not need a file extension.
However, for backwards compatibility reasons, scisr.php should probably be left alone and Scisr.php should instead be renamed to something else. Perhaps the Scisr class could be renamed to be more descriptive as well.