I honestly don't see the problem here. You did a run where you averaged low fuel consumption by running lean which the game took to be your expected fuel usage per lap. Come race, it took this expected fuel usage per lap value and multiplied it by the number of laps the race is to give you the recommended starting fuel load. However when you then started running standard or rich, you were suddenly consuming much more fuel than the expected value from your R&D programme, causing you to lose fuel/negative in the fuel delta/whatever you want to call it.
The best way to run this R&D programme is to run it how you would in the race i.e. no DRS and standard fuel mix and ERS. Using DRS lowers your fuel consumption average per lap, and running higher fuel mixture and lower ERS will increase expected fuel consumption per lap.