Not sure if others have been affected or it's only just me, but with this update, it seems I don't get credited for using most of the SoT in the Skull Quests.
Basically I did my usual "first off after daily click-over" routine. I play the (at least) 4 Skull quests that are waiting for me. I use the 3 "default" troopers you get and one of my normal troopers. This gets me the "Use 12 SoT" and "Use 3 Troopers" Daily Achievements.
After completing these 4 Skull Quests today, I'd only used 6 SoT according to the counter in the Daily Achievements tab.
Notes:
1. Since I played all 4 Skull Quests one after the other, I don't know if each contributed a bit, or it was just the last one (which cost 6 SoT) that was credited. It could be I got 1, 1, 2, 2 (instead of 5, 5, 6, 6).
2. I played 1 round of LoL Magus Lvl VII and it covered the Daily SoT Achievement for me.
This is minor for me but I thought I'd mention it, as accounting bugs like this become real problems with events.