Travis and others -
The best thing you can do is download the NetConsole plugin and install it. (See link under "C/C++ Team Update 4.0" on
this page). Watch the console when the cRio reboots. The messages are still a bit cryptic, but you should be able to glean hints about which pieces of code are complaining. You can then either change that code or just comment it out until you can get the rest of your code booting cleanly.
I too have seen a much greater sensitivity to little code issues that didn't seem to matter last year. Not sure exactly what the difference is this year. But I have found that using the NetConsole and the iterative process described above has helped get us through it.
Also, make absolutely sure that you have the latest cRIO firmware image and the latest WPILib update - the latest updates seems to have fixed a lot of the little stuff as well.
HTH.