Wow!!! Congratulations!! Great new look and feel!! It really makes sense to use the original Slic3er gui since it has been reworked.
I'm experiencing one issue reagrding the upgrade process from earlier releases on x64 Windows: The last release was installed under ~/Programs(x86); the new one under ~/Programs (as you can read in the release notes) . Starting Slic3r config within Reptier Host v0.7 it uses the executables from the old installation.
Renaming or removing the old installation folder solves this issue and the bundeled v0.9.1 Slic3r Version is used.