Part of his program is "entertainment value" to make sure the crew doesn't go insane from the tedium... And frankly staying fresh with vital new material for 150 people constantly... He must have been able to identify precise social clusters acting as stormwalls and safely regurgitate the same issues and developmental problems which would have crew running in circles to be his saving grace angel... 
Affirming busywork.
So any story we saw focusing on the Doctor was probably redone a few times to make the little people from the lower decks feel special, that they are part of the EMH's support network.
Or course, Janeway would have to be in on this, and certainly Kes, and maybe his other Nurse, Tom Paris.

Affirming busywork.
So any story we saw focusing on the Doctor was probably redone a few times to make the little people from the lower decks feel special, that they are part of the EMH's support network.
Or course, Janeway would have to be in on this, and certainly Kes, and maybe his other Nurse, Tom Paris.