It is hard to say what is happening with out the ability to see the code and the spreadsheet setup, but perhaps it is due to some calculation taking place on partially revised data.

Try disabling automatic calculation prior to updating the values.

Code:
Dim currentMode As XlCalculation
currentMode = Application.Calculation
Debug.Print ThisWorkbook.CalculationVersion

Application.Calculation = xlCalculationManual

' your code

Application.Calculation = currentMode
Application.Calculate
Debug.Print ThisWorkbook.CalculationVersion