While it is possibly true that you are not ready to tune your own edges, you are already knee deep, so I will try to help a bit.
It is likely your sidewall, it really shouldnt be shaving off, though, unless the board has had it's edges sharpened a lot. That being said, some boards do have the sidewall positioned to where this could happen. You want to get a sidewall cutter to cut some of that away. Some multi-angle side edge sharpeners can adjust to 6deg or so, that would allow you to shave away some of the sidewall, then go back to your 2deg setting and sharpen.
The best way to know if you have gotten all of the edge to the right angle is to run a sharpie down the length of the area to be sharpened. Once you are sharpening the edge, you will notice the marker going away as you work. Once all areas are clear of marker, you are done. Be careful, though, if you have a low spot and use this method, you will just be magnifying the low spot and can cause the board to ride a bit funny on that edge.
Just be sure you always have your tool set correctly, or the file clamped in correctly.