I’m going to guess the problem is as follows:
pi@raspberrypi:~/flotilla-offline $ /usr/bin/flotilla
/usr/bin/flotilla: error while loading shared libraries: libboost_system.so.1.50.0: cannot open shared object file: No such file or directory
Because we’re (still) not properly shipping Flotilla as a deb (we need to fix that) it has dependency quirks, since we’re manually copying in a binary built for a specific version of Raspbian (Wheezy/Jessie and now Stretch).
I’ll see if I can whip up a fixed binary for you to try out.