Quote Originally Posted by koopa
There's a quest rule to enable clocks, and one to set them to temporary (they go away after some time) or permanent (until you leave the screen). This can be set by the questmaker for custom quests. It seems clocks aren't turned on for the 1st quest.

Getting a clock while L4 cheats are active or you're using a keyfile can make it permanent, the other clock bug I found (I hope) and should be fixed in the next beta.
and in zelda classic v1.90 im almost certain clocks are enabled for the 1st quest.