Probably what you have run into is you have a preset table configured to automatically load. If you press the <Config IO...> button and go to that dialog and you have selected, say, Output 2 as "Discrete on Ch1/Fn1" then there is an extra button that will appear in the Function 1 box: <2: Preset>. If you press that button this takes you to a dialog called "Default Output Settings (Preset Mode)". This allows you to select a Preset Table for auto-loading. If you have selected a Preset Table for auto-loading (select "Load Table Table Number" with a corresponding number), then the CTRIO output (in my example, Output 2) will be selected for auto-load as "Discrete on Ch1/Fn1". What this means is when the CTRIO powers up, that particular Preset Table is loaded automatically (no Load function has to be called from ladders) AND the Output is automatically enabled.
Consequently, you do not have to use the Enable Output bit to enable the output. Also, if you happen to go into <Monitor I/O> function with the CTRIO reads of the PLC outputs suspended, you will notice the Output Enabled bit is already ON even though the <Enable Output> button is not pressed.
If you disable the Preset Mode function that automatically loads the Preset Table as described above by setting it back to "None", then you will not only have to manually enable the output (Enable Output = ON) to get it to work, you will also have to do a Load function from ladders.