This has happened twice now: 0 HP acquired. He's level 4 now and stuck at 47 HP.

The rest of the party gains the max, as I'm using all the mods listed at the very helpful guide found here (http://thunderpeel2001.blogspot.com/2009/01/planescape-torment-fully-modded.html).

I figure this is going to make the late game rather difficult. Anybody else experience this? Is there something I'm missing here?

yeah, you leveling differently as a mage/fighter/thief.
For example if you're a fighter level 7, mage level 5 and thief level 3, when you level as a mage from 5 to 6 (or 6 to 7) you'll gain 0 HP. The same for thief from 3 to 4 (or 4-5/5-6/6-7), zero HP.
When leveling as a fighter from 7 to 8 you'll gain 10 HP.
Also when leveling as a mage/thief from 7 to 8 you'll 10 HP.
After level 10 (in any class) HP gained per level is capped at 3 if I remember correctly.
Hope you'll understand.

It's because of your mods. In the unmodded game you always get at least 1 HP for levelling up. But the mods give you more hitpoints at the primary level ups, 47 HP art level 4 is a lot, you must have very high (16-18) con for this in the unmodded game.

Primary and secondary levels...I get it. Big thumbs up to mobutu and kmonster.