B12 is VERY difficult to regulate in the body because it is water soluble and and rapidly eliminated from the body. It is very difficult to overdose on B12, and takes a lot to cause damage. However, low levels are critical and can wreak havoc with the symptoms you describe. Constant monitoring is key until you and your doctor can find the right dose and timing of the dose to stay level.
It can be difficult to track down the reason for low levels of B12. Pernicious anemia is rare and one cause, but a more common cause is that medications can also cause interference of the absorption of it. Regardless of the cause, it should be treated and to stay on top of it. It sounds like your doc is doing that and ask for testing again to make sure the new dose and timing of it are keeping you level. It should be taken right before your next dose, which is called the trough (lowest) level in your system, as opposed to the peak (which is right after your last dose ) this is not a helpful indicator.
Good luck finding the right dose and when the doses need to be spaced apart to keep it level.