From what I’ve read, the manumission process was involved and time-consuming, which was the reason for the delay between when Lee inherited the slaves and when the last of them was actually freed.
From what I've read by the terms of the will the slaves had to be freed within 5 years of Custis's death. Custis also left a lot of debts so Lee would up freeing them over time, and in the interim he rented them out and used the income to repair the family finances. He was two months late in freeing the last of them but since it was in the middle of the Civil War and he had his attention on other things then we can't blame him for being just a little tardy.