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.