I believe you need to set the status date to the start date of the work being baselined, then set the baseline.
I noticed this issue when updating resource costs and then running earned value report. When the baseline was set with a status date of today, the costs did not change correctly. however when I set the status date to the project start date, then baselined, the cost was correct in earned value.
This was on Project Server 2013 so it may be different, but the situation sounds similar so hopefully this will work for you as well.