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There are a couple of reasons Christ used leaven in a positive sense regarding the Kingdom of Heaven.
The Catechism of the Catholic Church (CCC) teaches
CCC-2832 As leaven in the dough [bread in the Lord's Prayer], the newness of the kingdom should make the earth "rise" by the Spirit of Christ.
CCC-2660 Prayer in the events of each day and each moment is one of the secrets of the kingdom revealed to "little children," to the servants of Christ, to the poor of the Beatitudes. It is right and good to pray so that the coming of the kingdom of justice and peace may influence the march of history, but it is just as important to bring the help of prayer into humble, everyday situations; all forms of prayer can be the leaven to which the Lord compares the kingdom.
The idea behind associating leaven and Spirit and Kingdom was the pouring out of the Spirit at Pentecost. Pentecost, unlike Passover where no leaven was present, called specifically for leavened bread.
Ex. 12:8 [at Passover] And they shall eat the flesh in that night, roast with fire, and unleavened bread; and with bitter herbs they shall eat it.
Lev. 23 17 [on Pentecost] Ye shall bring out of your habitations two wave loaves of two tenth deals: they shall be of fine flour; they shall be baken with leaven; they are the firstfruits unto the LORD.
With leaven, with the Spirit, the Gospel of the Kingdom would spread from Jerusalem, to Judea, to the ends of the earth.
Mark 16:15 And he said unto them, Go ye into all the world, and preach the gospel to every creature.
Acts 1:8 But ye shall receive power, after that the Holy Ghost is come upon you: and ye shall be witnesses unto me both in Jerusalem, and in all Judaea, and in Samaria, and unto the uttermost part of the earth.
So, depending on the context and application, leaven may be see both negatively and positively.