Does anyone know if it is the beginning of Season 4 or the end of season 4 that Cuddy starts to have feelings for House? Or does it happen in Season 2 or has it been that way the whole time?

I believe their feelings for eachother started wayy back, when they were in collage.
the writers, though, started developing their relationship only in season 3 (after they got tired of Hacy&Hameron)

To me, there has always been something flirty between them from the first show. I think feelings between them really started to ipakita in season 3 though particularly after she lied on the stand to protect him.

AS I SAW ALL 6 SEASONS OF HOUSE M.D ..

THAT I FOUND .. THAT KIND Of pag-ibig BETWEEN HOUSE AND CUDDY ,, WHAT I WIIL WRITE NOW IS I CAN'T FIND THAT WORD TO DESCRIBE THAT pag-ibig BETWEEN THEM ..

THE FEELING START FROM THE BEGINNING ,, SEASON 1