You are using SublimeLinter instead of sublimelint right?
If using SublimeLinter
Try to do some debugging:
look at the message of linting a file via "console" ( be sure to navigate to the folder )
php -l filename.php
and compare the output with the result on sublimeLinter.
on line "for line in errors.splitlines():"
maybe there is a need to adjust the regular expression
add more prints as necesary to check where is failing.