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Re: Need to manually reboot cRIO to download code
Our team was having the exact same problem!
Now, everytime we re-download code to the robot, we make sure we have the Driver Station opened in the Developer account, close out of it, then click run. Once Netbeans goes through all its stuff, reboots cRIO, etc. It will get to the line DisableInit() completed. From there you can re-open the FRC Driver Station and everything should work perfectly. Hopefully this bug of ghost code is fixed! 
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