A couple of questions (or things to test) first of all...
1. Can he clear fine while going down the line feet-first?
2. What sort of depth does he typically reach before finding he can't clear any more?
3. How is he equalising? (I.e. what technique? Valsalva? Frenzel?)
If he's fine feet-first down to 6 or 7 metres (and maybe even head-first heading towards that), but then struggles after that, it would suggest he's using Valsalva to equalise, rather than Frenzel. As a scuba diver, he may very well be using Valsalva, since having lungs kept (reasonably) full of pressurised air makes it easy to use muscles in the torso to create the necessary pressure to push air up into the nasal cavity (i.e. the Valsalva technique).
Unfortunately, though, this becomes more difficult to do as a freediver, since the air you take down in your lungs gets compressed as you descend – and it's hard to push air from your lungs when don't have so much (volume of) air in there (try it: blow out the air from your lungs, then try to keep equalising using Valsalva and letting a little air escape each time to simulate air compressing in your lungs as you get deeper). This is why freedivers typically use Frenzel instead. That technique uses muscles in the throat and back of the tongue to 'squeeze' air up into the nasal cavity, rather than using diaphragm/chest muscles. (It's also more efficient, using less oxygen, which is obviously a good thing if you're holding your breath...)
If this is the case then the answer is obviously to learn Frenzel equalisation – there are a number of tutorials that can help (youtube vids, etc.) And if he's actually doing (or planning to do) a freedive course then his instructor should be able to give more interactive/hands-on help.
Conversely, if he is already equalising fine to greater depths while descending feet-first (e.g. beyond 10m, even 15-20m), but finds it difficult to equalise head-down even near the surface, then there could be a few reasons:
1. check that head position is right while descending – don't look down the line towards destination, but keep head straight, looking at the line (tilting the head back stretches the neck and muscles of the face near ears, making equalisation more difficult);
2. and/or it could be that relaxation is more difficult (it's not so easy to stay relaxed while upside-down, so that can cause some muscles to be more tensed up, which can reduce ability to equalise);
3. and/or it might even simply be due to gravity causing structures in the head & ears to be not quite the same as when upright.
In all of the above cases the answer is to experiment and practice...
Start by swimming down at a shallow angle (or even just sinking by blowing air from lungs), and see if being at that shallow angle makes it easy to clear the ears. If so, swim(/sink) a bit steeper, just until you start to find it gets a bit harder. Then spend some time practicing clearing while heading down at that angle. Once it become easier, try going down at a slightly steeper angle. If you find equalising is difficult head-down within the first 2-3 metres then you don't even have to be in deep/open water for this - just a local pool that's deep enough for you to find you struggle with equalising while going down at some steep enough angle.
You can also use a pool to practice equalising while upside-down (or at some angle) by hanging your head over the edge and with legs on the side of the pool (can help to have a buddy holding your legs - but really should have someone with you anyway if you're holding your breath in the pool).
There could be a couple of other things I've missed, but those were the two main directions that came to mind off the top of my head (first ensure using Frenzel, and then practice at increasingly steep angles until vertical).
Hope that's helpful!