And they are still dimmer than they should be when I set every io to high.
How do you know how bright they should be?
A multiplexed LED will always be dimmer than one on all the time. It is the ratio of on to off that determines how bright it looks. This is known as the duty cycle, so if it is only on for one 10th of the time it will only be one 10th as bright. Well not quite because of the non linearity of the eye, but if it is only on one 10th of the time it is like putting one 10th of the current through it.