K.M.
Ok, I don't know if this will work. . . BUT my dad used to put my little sister to sleep every night. How he did it was he promised her an airplane ride. So what he did is once she got her self ready to finally go to bed. . . she would stand on a chair in the living room and yell "airpane, airpane" then my dad would make engine sounds and she would stretch her arms out to the side. He would then put her on both of his forearms and fly her around the house to her bed for nighty-night. He would then read a book to her and she would go to bed. If she got up. . . she didn't get airpane the next night.
Good luck. I hope this helps. Maybe he just needs a separate daddy routine for bed time and that will solve the problem, Something special just between the two of them.
Also, it may be a security problem. Mommy means security, not daddy, so maybe he just doesn't feel as secure with JUST daddy home. Maybe let him sleep with one of your shirts or something that reminds him of you for security. Those are the only suggestions I can think of.