The boost is not changed under active effects, but it should still be there. Also, have you encounterd any wispmothers?

On the first post character..yes.  I did the Pale Lady quest while wandering around.

On the second post (level 30), I don't think I did.

As noted, on both, I took the potions and then the stone.  Magicka runs out and spells break. 

Weird, worked for me. Though, wispmothers can cancel out the glitch, for some reason

Is it possible the cheat code added potions won't work even though the percentages are the same? Should they show up as Draught and Philter the Healer? Maybe only the loot versions show up like that?

It's Exlixir of the. Healer, not. Draught you need

The build shows Draught and Philter...

I used an Elixir, and it worked, strange

Doing just 1 or the three potion combo?

I just. Added the elixir x2 and did elixir/Philter/elixir. Still showing just 50% bonus and spells die when magic runs out.

Do I also have to have the advanced perks to do this?

PS: Both characters I tried this step, still run out of magicka and spells die.

So the build says this:

Once these three potions have been collected you need to program the atronach stone with the following potion combination when selecting it…

Philter + Draught + Philter -> Select Stone

You're telling me that's wrong?  OK, back to try the opposite that you posted.  I'll let you know.

Just curious, if you are wandering (as the build RP suggests) then how do you stay away from wispmothers?  And if you do fight one, can you reset the "bug"?

(EDIT: Nope, tried your order as well with no success on either character.)  The only thing different is these are "added" potions through the PC command.  I'm at a loss.