Wow! I was going to start a new thread tonight, but found this! I JUST got my RTV X900 back after a month because of the same problem - but worse! I have 240 hours and 1148 miles on it and my machine had the exhaust b pipe break from the exhaust manifold flange just like yours! I called the dealer (my machine is only 7 months old) and told them that it looks like the exhaust pipe is only press fitted into the flange and it has failed. Two days later I had to park the machine because the cast flange (aluminum) of the transmission that supports the forward muffler bracket fatigued and broke!
Kubota first balked at accepting that it is a design flaw and said I must have backed into something. I couldn't believe it- no damage to the rear most muffler bracket or tailpipe!
Fortunately my dealer had kept my email messages and with the no evidence of rear damage they finally agreed to weld the forward muffler bracket and then welded the exhaust pipe to the flange as should have been done originally. When the dealer dropped the machine off I said that I bet that Kubota will have more trouble with this exhaust problem.