Check the CoilSystem:Cooling:DX object that's created in the idf referencing the two stage coil - it is missing the inputs 'Dehumidification Control Type' and 'Run on Latent Load' required to get the coil to control for humidity.

To get those inputs, you'll have to use an EnergyPlus measure, the relevant code for which I've included in this issue documenting the defect.

Edit: In the Measures tab of the OpenStudio Application, bottom right there is a button with a green plus sign to 'Create Measure from Template and Add to My Measures'. Click that, a window will pop up to 'Create New Measure'. Enter name, etc, and change the Measure Type dropdown to 'EnergyPlus Measure'. The rest is optional. Click 'Create Measure and Open for Editing'. A file explorer window will open with the measure folder. Open measure.rb in a text editor, and replace the template code (lines 46 - 85) with the code from here. Delete lines 28-32 (no longer needed). Save the file. In the app, find and drag the new measure from the right-hand library pane to the 'EnergyPlus Measures' drop area. Run your model and verify it's working.