Odd indeed. I'm not sure of the B6 but I know that some bikes come with a switch that cuts ignition if the bike's inclination changes drastically (as when you tip the bike and fuel is going everywhere). If the B6 has one, it could have been triggered going up and down the trailer. It should have returned to its normal off position once the bike leveled, but yours may be stuck. Try finding it and bypassing it.
Alternatively, I would look into other loss of ignition sources which may have nothing to do with the bike's transport. Before anything, check battery voltage and do a load test. Then try starting the bike with the kickstand UP, clutch IN, and in neutral. If the problem is starter related, you could try push-starting the bike. After all this, I would check the ignition switch and the kill switch. I hope this helps.