After having fought a paladin I seemed unable to get
the healing benefit of berserk. The hit dam bonuses were still
given. I have not experienced this behaviour with berserk before,
I don't know whether it is a bug or not.

I was in the middle of some fighting, so I don't have complete logs
but here are some snippets:

>>>
700hp 277m 805mv 8910tnl 6 PM water aff
You are affected by:
Spell: 'protection from good' for 19 hours.
Physical malady: 'boneshatter' modifies dexterity by -6 for 10 hours.
Physical malady: 'boneshatter' modifies strength by -6 for 10 hours.
Spell: 'nightwalker' for 8 hours.
Physical malady: 'angels wing' modifies strength by -4 for 5 hours.

700hp 277m 805mv 8910tnl 6 PM water berse
Your pulse races as you are consumed by rage!

700hp 247m 755mv 8910tnl 6 PM water s
>>>
My max hp is around 1000


Later, again after having fought the same paladin:

903hp 356m 852mv 8908tnl 4 PM civilized berse
Your pulse races as you are consumed by rage!

903hp 326m 802mv 8908tnl 4 PM civilized

Spell: 'armor' modifies armor class by -20 for 12 hours.
Skill: 'berserk' modifies armor class by 24 for 7 hours.
Skill: 'berserk' modifies damage roll by 9 for 7 hours.
Skill: 'berserk' modifies hit roll by 9 for 7 hours.
Skill: 'nightfist' modifies damage roll by 8 for 6 hours.
Skill: 'nightfist' modifies hit roll by 8 for 6 hours.
Spell: 'lightningshield' for 3 hours.
Spell: 'lightningshield' for 3 hours.
Spell: 'fireshield' for 3 hours.
Spell: 'fireshield' for 3 hours.
Spell: 'frostshield' for 3 hours.
Spell: 'frostshield' for 3 hours.
Spell: 'oozeshield' for 2 hours.
Spell: 'airshield' for 2 hours.

>>>
I couldn't see any special affects. I asked the paladin if he had
some special ability to prevent healing, but he didn't know of it.

I'd guess they used light of heaven on you dispelling the berserk. That would dispel the berserk, but not allow you to re-use the healing piece of the berserk.