The stats count, but it only uses the stats for a lesser mutagen version if you use any mutagen better than that. You lose the net gain in stats from a better mutagen anytime you load a new zone or reload save game. (you can fast travel on same map without loss, just no zoning or loading save file)
1. equip a lesser mutagen to see what your base stats are
2. equip a better mutagen of that color - normal or greater for example - will see increased stats, as expected
3. zone to a new map or save/reload game
4. if you are affected by this bug, then you'll see your stats reset to the base or lesser mutagen bonus
The best way to describe this condition is that you do not lose your mutagen buffs, just the increase you get from using a better than lesser mutagen whenever you zone map or reload game. In short, makes you have to constantly manually remove and replace every mutagen whenever you travel maps or reload (excluding fast travel on same map)
That's not what is happening for me btw.
I checked this out.
Right now, I'm in my second playthrough, experimenting with a sign build, I'm level 11. That allows me to use 2 mutagens and 6 ability slots. I have 5 of those 6 ability slots filled with blue skills, the other one with a neutral skill (medium armor passive). Both of my mutagen slots carry a greater blue mutagen.
Right after loading the game, I have +103% Sign Intensity (wearing all of the basic griffin armor + talent).
Now if I replace one of the greater blues with a lesser blue (the one linked to 3 blue abilities) , I actually drop to 93%, removing it entirely gets me to 73%. Putting the greater blue back in, gets me to 113%.
So equipping a lesser blue one coupled with 3 blue abilities gives me 4*5% = 20%, which seems fine. Re-equipping the greater blue one gives me 4*10% = 40%, which seems fine too. The "intermediate" value right after reloading the game however is a 30% bonus, which is just odd. That doesn't even match the 4*7% = 28% I should get from using a medium blue mutagen.
But: Possible explanation to the rescue!
What happens if I unequip my other greater blue mutagen which is only linked to 2 blue abilities? I drop from 113% to 93%!
Putting a lesser Blue mutagen in place puts me to 108% (3*5%) and equipping the greater blue mutagen again gets me to 123% (3*10%).
So, what seems to be happening here is that after loading up the game (or reloading a savegame) the mutagen-slot itself doesn't work at all, but I still get all the linked bonuses.
So in case of my 3-linked greater blue mutagen I receive 3*10% = 30% and in case of the 2-linked one I receive 2*10% = 20% and re-equipping them makes the mutagen itself in its slot work again, giving me my missing 10% sign intensity in both cases.
To back this theory up, I simply equip a lesser blue mutagen in my 3-linked slot, save the game and reload it. Result: I end up having +88% sign intensity. unequipping it makes me drop to 73% again and re-equipping it gets me up to 93%. So, as we can see, after loading the game, my lesser blue mutagen, linked to 3 blue abilities, just gave me 3*5% = 15% bonus instead of 4*5% = 20%, which seems to indicate, that the mutagen-slot itself is simply not working after loading a savegame.
edit: One final test: I dropped all my abliities linked to the 2-linked mutagen (even the neutral one) and just equipped a lesser blue mutagen to that slot. Saved the game, reloaded and had +63% sign intensity. Removing my lesser blue mutagen didn't change my sign intensity bonus at all in this case, so I think I can safely assume that it's the mutagen slot itself, that doesn't work after reloading the game, until you re-equip your mutagens (but any present links to that mutagen still work as they should).
Maybe someone would like to check this in his game.
TL; DR: Performed a series of tests, that showed, that it's actually the mutagen-slots themselves losing their effect after reloading the game, no matter which level of mutagen is equipped. The linked abilities however still provide their expected bonus.