I stopped by the dealer and told them I would do it myself and they gave me a free tube of caulk.
I will probably buy a roll of Eternabond and redo all the seals. Last trailer (that we bought used) died from a water leak in the back corner. I couldn't find any obvious signs of leaks but there was obviously one somewhere! I'll be a lot more anal with this one.
I showed the dealer the pic of the rear roof seal. They said it didn't look like a problem but since it is new and under warranty I should probably bring it back and let them inspect. Everything looks sealed up with the exception of the part that the sealant failed and I can't tell where any water intrusion would have happened without actually pulling the entire black piece off and pulling up the roof membrane... which I'm not going to do on a new unit.
Interestingly enough it looks like plain clear silicon caulk that they used at that junction. Haven't decided if I will just recaulk it or take it down the dealer for them to inspect. Would hate to recaulk it and then some problem comes up later in the life.