Why will my MG44 show microns when directly hooked up to pump but not when I am pulling on a system?

Evacuation takes time. You are pulling a vacuum in a larger volume (ac unit + vacuum pump) compared to just a vacuum pump. Check that there are no leaks in your hoses, change the oil of the vacuum pump, and perform a triple evac if there is an indication of a lot of moisture in the system. Change the oil in the vacuum pump