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.
I've waited for version 0.14, but nothing happend automatically (I didn't have reconfigure checked - was this cause?). So I installed it manually with above command.
But now, GUI on phone is garbled, many copies mixed one on another only on upper half of the screen ?
Do you see the same ?
I will regenerate all Orbiters and will see if that helps...