My PRO2 plunger stem is crooked.

When brewing, the stem appears to be tilted, or the lever roller isn't hitting it centrally.

The stem is designed to tilt any direction up to 5 degrees without having an impact on your extraction. Our rule of thumb is that if the roller is hitting the center of your stem's top coin, even just grazing the center point, it is within this allowance. Additionally, the weight of the gauge sometimes pulls it to one side: Just set it in its most upright position prior to the start of your pull. 
If you find the stem to be tilting beyond this described tolerance, or the roller to be contacting it too far to one side, the portafilter holder itself may be misaligned. In order to realign your Flair, please reference this video, which shows how to loosen and reposition the portafilter base.