I'd agree with that too...kills the strategy of aiming for a colored square then solving. Why they didn't just keep the original Bonus Sprint format is beyond me. Scattergories' jackpot was pretty paltry too (started at $4,000, divided amongst four people).
So here's the things about that: The pink/blue square money was going to be given away eventually, just not necessarily to the player who landed on them. Reducing the starting point from $5,000 to $1,000 means the show saves $4,000 every time the Bonus Sprint is won, but it looks super lame that the bonus round is played for as much money as what was given out in the Sprint round a few minutes ago.
But the thing that just kills me is that bonus squares feeding the jackpot takes away one of the great things from the original show: when somebody would say "I think I know it but I'm going for some money, Chuck." The crowd would erupt into applause. Sure, it's the same $500 and $1,000, but the money doesn't go straight into your pocket anymore, you have to jump two hurdles to get it.