This is deliberate. Originally, the timer for the dam closing was removed as soon as you got the codes to close it whenever you want (since there's no longer a need to time your arrival at the dam). However, it was pointed out that since you don't get the time limit for Santorini exploding until you've seen it explode twice, it'd be nice to keep the dam timer until you get the Santorini timer. Once you have the Santorini timer, there's no use for the dam closing timer anymore. The dam opening timer remains, since that can still affect you (if you're part way across the dam when it reopens).