Are you running the latest cRIO image for Java? Looking at these two lines of output...
Code:
...
[cRIO] * Loading FRC_JavaVM.out: FRC_JavaVM
[cRIO] ...FRC_JavaVM failed to load.
...
...suggests a library is missing on the cRIO. The other thing that looks suspicious is the number of messages regarding the OTA Server. Remember that when you download a FRC Java program to the cRIO for the first time you will need to reboot it manually. I'd look into possibly re-imaging your cRIO though.