This is a bug, so it need a support answer, but I am also posting the topic here for other players.

Page 22 of the manual mentions at the bottom:

Mana
Mana is magical energy that you use when casting spells. Each
spell drains your mana, and if your mana total is too low you
cannot cast any more spells.
You can regain your mana by consuming potions or herbs with
high magical properties. You can also regain your mana in places
of great magical significance, but only if you know how to tap the
energies of the magical place.

Having progressed into the game but not found anything about this yet, and running now on a chronic mana shortage (potions are just not enough), I started investigating the issue, and found a very good walkthrough which explained that you need to 'touch a Hex stone once you have access to the Hex'.

This is clearly not working for me, the ONLY time I get some mana from a HEX stone (and not much) is the very first time I touch it, at the same time as the character starts teleporting.

It IS a feature referred to in the manual, therefore that is definitely a bug.
I found that there used to be a website for this game (expired) where official patches whoudl have been mentionned, and found references to www.gamespot.com to patches for this game (but cannot find them).
I therefore suspect that the current GOG version is not fully up to date, and I hop that GOG staff will investigate this.

An answer here from them would be appreciated.

Well, the first reply from GOG's support was that they were not aware of such mana regeneration feature, so I asked them to read BOTH the walkthrough found at http://www.gamefaqs.com/pc/913680-soulbringer/faqs/19885 (which explicitely mentions it several times through the FAQ and walkthrough itself) and page 22 of the manual coming with the game, which explictly refers to the existence of such a feature, without stating what it was.

The reply I received back was:

'Hello,

In both manual, and FAQ there isn't any explicit about multiple usage of Hex Stones to regenerate mana. In fact, this is how the game works currently and we won't be able to change anything for you, because GOG didn't develop this game. I'm sorry for inconvenience.

If you find out that the game is to difficult for you, you can try using these cheat codes:
(To access command menu press "/")'
... followed by a list of cheat codes.

So, basically, what we have here is a support which cannot be bothered to actually verify (they cannot have read the walkthrough and write this statement), and/or do not want to do their job; aka 'cop-out'.

In the walkthrough there is one part that says

"Head west. On your way, return to the sacred grove and activate the
hex stone. You'll get experience and your spell points recharge.
Continue through Ravenscar, and north to the Path of Shadows. You can
activate the hex if you desire, but you may find it more advantageous
to save it."

when it says you might want to save it, I assume it means the mana recharge only works the first time. No where does it expicitly stae that hex stone recharge mana everytime they are used. This is also what gog said. I have not gotten that far yet, due to compadibility issues, but it seems to me that this is likely intended, likely to make the player think about if he really wants to activate that hex stone now, or save it for later.

Edit: based on this review it seems like it is intended:

http://www.escapistmagazine.com/forums/read/326.178061-Off-Topic-Reviews-Soulbringer

It says:

" Those hex stones (large magical sculptures, basically), in fact, wind up being the game's multi-purpose tools, serving not only as compass landmarks, but eventually as teleportation points, gateways to the five magical worlds, and one-shot mana replenishment stores."

This site seems to infere the same thing as the walkthrough, though it claims your mana is fully regharge at the hex stone:

http://home.alphalink.com.au/~dannj/soulbringer/soultips.htm

"The deep desert may prove draining on your mana. You may want to hold off from touching the Hex stone near the entrance to the deep desert when you first encounter it. That way, you can drain your mana completely flinging spells at krakens (chose your spells carefully and you'll balance your SECULORUM as well). Then head back to the stone, touch it for the first time, and your mana will be completely restored. That way you save mana potions. "

I am unsure if only a few hex stones replenish all your mana or if there is some other reason for it, but it is clear that the hex stones only recharge mana the first time they are used.

Wait! Tech support told you console mode works?! Some of us cannot get it to work! =(
(I just want to use it until I get to point in the game I reached way back in the day, when I got hit by a game killing bug while trying to leave the desert.) https://www.gog.com/forum/soulbringer/getting_the_console_to_work/page1