Once I do graceful restart from whm. It restarts and when its back online, the whm status page says

everything is up and green lights :)

but
apache (1.3.26 (Unix))
bind (9.2.1)
Anotherone

They were the only ones with the redlight and said it was down, but acessing webpage still worked, it took about 10-15mins before they turn green, ive reset the server like 3 times, each time the same thing.

Is this normal?

I dont know if I would like to call it "normal" but it is usual with WHM

did you tried to restart those service and to restart chkservd?

Do a shutdown/Reboot without a disk check.

See if that does the job.

Robbert