Setting up the environment. That was our biggest struggle. If you follow the steps outlined
here (word for word), it should be all good :) It took us about half the build season to find that. Once you're set up and the cRio has the C++ image, the template code in WindRiver is more than good enough to get you started. One other problem we had was keeping up to date with the updates throughout the season. You don't get much (if any) warning, so check FirstForge every so often and make sure you didn't miss anything. If you get to the competition and forget to get the updates, there's usually someone with all the updates on a flashdrive willing to share with you :D
[edit] also, it can get pretty frustrating if you don't specify module numbers when initializing stuff. If you're sure everything is set up right (the driverstation says the cRIO and robot radio are GOOD), try switching the module numbers. It defaults to the first module available, but that's not always the one you're using (like many cases when using an 8 slot cRIO). Normally you don't need to specify.
Code:
something=new thing(module_number, port_number);