I get the following since Naomi upgraded a few days ago. Always when opening ST3 from scratch, and sometimes when switching projects or even buffers. 
I am using Windows 10.
In addition, there is no syntax highlighting on any of the filetypes i use which Naomi is supposed to handle anymore - not only PHP but SASS and React are affected. The error message, however, always references the PHP syntax file.
There is no code required to reproduce; it happens spontaneously when opening the ST3 main program, and intermittently thereafter. Below is a list of the other PackageControl packages I am using, in case there's a known conflict:
- DoxyDoxygen
- GitSavvy
- LESS
- Origami
- PackageControl
- SideBarTools
- SolarizedColorScheme
- SublimeLinter
- SublimeLinter-contrib-lesshint
- SublimeLinter-contrib-sass-lint
- SublimeLinter-eslint
- SublimeLinter-phpcs
- SublimeLinter-phpmd