I checked the code. We check the "Reconfigure Device" flag after the bluetooth dongle links to the phone--which can only happen when it connects to the software. So, checking Reconfigure Device will cause it to re-send the app to the phone, but only if there's already another version running on the phone. I fixed the logic, so in the .14 build, it will also check the flag upon detection of the phone in cases like yours where there is no version on the phone.
So, to manually force it to install... Login to the box that has the bluetooth dongle and run this command:
/usr/pluto/bin/PhoneInstall.sh [mac address] /usr/pluto/bin/Pluto_S60.sis
where mac address is the mac of the phone.