As a first thought, this could be due to a different structure on the stars themselves.
Let’s take a simple example: You build 1 Industry each on 4 stars, Sneferu builds 2 Industry each on 2 stars.
At Manu 1, one Indu produces 0.25 ships per tick. After 6 ticks (1 jump) each of your four stars produced 1.5 ships, however only 1 for each materialized yet. So you produced 4 ships. Sneferu produced 6 ships in the same jump (3.0 stars on each of the two stars) with the same number of Industry.