We are having a similar issue: we are unable to get inputs or set outputs through the cRIO. However, we are not getting the "Digital module 1 is not present" error message. You can use code like the following to detect module presence:
Code:
for(int i = 0; i < 2; ++i) {
System.out.println("digital module " + i + ": " + ModulePresence.getModulePresence(ModulePresence.ModuleType.kDigital, i));
System.out.println("analog module " + i + ": " + ModulePresence.getModulePresence(ModulePresence.ModuleType.kAnalog, i));
System.out.println("solenoid module " + i + ": " + ModulePresence.getModulePresence(ModulePresence.ModuleType.kSolenoid, i));
}
We *are* seeing this error message as well:
[cRIO] DIO LoopTiming: 260, expecting: 261
[cRIO] DIO LoopTiming: 260, expecting: 261