When you activate Breath Of Heavens with mentioned rune, there is a an icon showing time left for the additional spirit increase. It counts down the 5 second period.
Now, if you attack using normal left mouse click, everything works correctly. BUT, if you use SHIFT + left click(primary attack), the countdown is INSTANTLY disabled and the countdown icon is no longer visible.
You can easily reproduce it by activating mentioned BoH + IwL in an empty room without monsters and during the 5 second countdown period use shift+left click, the countdown is instantly stopped.
I'd like to say that it's very disappointing because this is definitely not the only bug i came across.