The energy output of Diesel and Refined fuel in a combustion engine is 3 RT/t and 6 RF/t respectively, shouldn't it be 30 RF/t and 60 RF/t, based on what I remember in old traincraft it output energy in MJ not RF and 1 MJ is equal to 10 RF, so shouldn't the energy output be higher?

Yes. You're absolutely right. This is our mistake. We just ported the old values and never thought about that Buildcraft changed from its MJ to RF. Thanks for the hint!