Both yesterday and today I had the same problem Ease pain took the purity seal and started its' cool down. My total seals reduced by 1 but I never got the extra 2 the skill was supposed to give. The error yesterday was after Caspian did the manual reset so I figured it was a wash.
It happened again today I had 11 seals before 12EST I collected the seal after the reset which brought me to 12. I attempted the skill Ease pain upon the refresh of the screen and I was back to 11 seals and ease pain was on cool down.