Unlike any other building of similar type, the first level factory for Synthetic races offers a FLAT modifier of 0.01 units per level for adjacency bonuses. All other factory and research buildings use MULTIPLIER modifiers here.
This obvious bug can be fixed in ImprovementDefs.xml like this:
1. Search for the line <InternalName>ManufacturingYor</InternalName>
2. then locate the group <LevelEffectStats> within this improvement definition
3. change the line <BonusType>Flat</BonusType> within this group to <BonusType>Multiplier</BonusType>
P.S.: this refers to GC3Crusade. I don't know if this bug is still present in later expansions.