Some ideas for you: try to take a temp reading of your sample at the same time you check gravity. Even if you take into account what the ambient temp is, doesn't mean that's the temp of your sample and also your equipment may absorb or give off heat depending on their temp. (Ex you just took them both out of a cold sanitizing solution)
Second, when you so have your sample, cover the opening of it and shake it to cause it to foam. Do this a few times and let is settle out. This way you are forcing carbonation out of your sample.