Fixed!

Our subcontractor came over yesterday and confirmed that the crack in the tile was causing the leak into the kitchen.  There were apparently two reasons for this.  One, the grout was a non-flexible kind of grout and two, the cement board was only nailed to the wood underneath instead of screwed in, which allowed for more flexing of the tile.  So he regrouted the cracked areas, screwed in the cement board, and even repainted the kitchen ceiling!  (I know that shouldn't be a surprise, but I wasn't expecting it at all.  What does that say about the low expectations we have for contractors?  That's why we like this guy so much!)