Thanks for the hint. I did release an update of FuzzyFilePath (for Sublime Text 3), containing bugfixes and some more options.
Details on the new settings are documented in the README. Two of these options are
I hope this works as expected and may solve your issue. I also added FuzzyFilePath configuration to the Menu in Sublime Text | Preferences | Package Settings | FuzzyFilePath. This should help managing the configurations.