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Hi @zoe.baker-bushby,
you're right and I've the exact behaviour now.

I simplified the rule, and just switching between model states causes the issue.
 
Create another model state named "Model State1" , add and run the rule, first time it runs then nothing.

	MessageBox.Show("START")
	Dim doc As PartDocument = ThisApplication.ActiveDocument
	Dim modelStates As ModelStates = doc.ComponentDefinition.ModelStates
	Dim masterMs As ModelState = modelStates.Item("Master")
	Dim ms1 As ModelState = modelStates.Item("Model State1")
	ms1.Activate()
	masterMs.Activate()	

 
@johnsonshiue could you look into this?