I want it so when 60 seconds is up it blinks once and then when 60 seconds is up again it blinks again, same with hours please.
Blinking is not something a pin can do. A pin can turn on. A pin can turn off. By turning the pin on, pausing, turning the pin off, pausing, and repeating, the LED connected to the pin can appear to blink.
So, far, you haven't defined how long the pause while the pin is on should be, so the fact that it is not to your liking is hardly surprising.