It sounds to me like you're not actually downloading code to the robot. This could be because you have something configured wrong or simply because your code has errors and isn't successfully compiling.
First, make sure when you build your code that it's successfully compiled. There will be lots of red and error stuff in the windriver output window if it hasn't compiled.
Next, make sure you have the cRIO, your laptop, and windriver configured correctly.
Go to the
Imaging your cRIO Guide and follow it step-by-step. That will make sure that your cRIO and laptop are setup correctly for C++.
Then go to the
Building and Downloading a project to the cRIO Guide. I'd recommend doing "Building a robot program" and "Verify that no User Code is running". Then skip ahead to "Loading a program to run on robot startup" and follow along till the end. Running in debug mode is a little more complicated and error prone than just deploying and rebooting. Hopefully after you reboot your robot, whatever code changes you've made will now show up on your robot.