I believe you're fixating too much on the number on the bar and assuming that this number correlates to you getting bigger/stronger.
Keep in mind that deadlifting in a fatigued stated is still making you stronger, you're just witnessing less weight on the bar. As you've already observed, when you AREN'T fatigued, you ARE able to lift more. Thus, if you get stronger on your deadlift in a fatigued state, it will mean also having a stronger deadlift in a NON-fatigued state.
You're never going to be 100% fresh for every single movement in a routine, but as long as the conditions that you train each movement remain constant (ie: you always train deadlifts after squats), as long as you are witnessing increases in those movements, you are getting stronger overall.
I do not feel you need to change your programming to meet your goals.