I use lineup with kazekage gaara, shikaku, and windmain, while i use the chakra generation, on turn 2 when I pop my Gaara's mystery it generates enough chakra to pop both giant rasengan of Windmain and Shikakus mystery. though even though I press them right away after the chakra is generated, most of the times the game proceedes to do gaaras reguler atttack, sometimes even more attacks of more ninjas instead of proceeding to cast my queued up mysterie.

Hence I think it affects mysteries being queued after chakra generation