I would send an e-mail, something along these lines. "per our discussion on Feb. 23, 2012, I let you know my concerns regarding the data that we are receiving. My concern is that the data is incorrect. I will follow your instructions and continue until further notice".
Print this out and put it in your folder for documentation. Also, request a receipt so that you know when they open it. Also, send an e-mail to your boss "I wanted to let you know that I have concerns about the data. I do not want this to reflect negatively against me, especially since I am working under the EIP. I want to make you aware of the issue. I will follow your instructions."
Also, print a copy of that as well. You need to document EVERYTHING. If it verbal, send an e-mail, "per our conversation on whatever date, we discussed" then list what was disucssed. Always keep a copy for yourself as well. CYA needs to be your motto!