We've discussed the nuances of scanning watercolor paper quite a bit on this blog in the past. Ted observed that turning a watercolor paper 90 degrees helps at times if a scan is not showing up well. I have a trick I'd like to add
To get a "flat" scan on bigger pieces that might have a few visible bumps in your scans just turn the paper art side down on a towel and mist it with water, soak up any small pools with another towel and then repeat until the paper gives in and lays flat. Then just scan it in slightly wet.
Obviously, be careful to not get the art side wet in any way. It should feel dry.