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To put is simply : the refresh of the conditional formatting is only performed the the worksheet changes when the calculation mode is set to manual.
If the calculation mode is set to auto then of course all formatting is updated immediately. I have attached a sample file to demonstrate this point. Theoretically, conditional formatting needs to perform calculations too, so that it stands to reason that Manual Calc settings will not change instantly the settings of your sheet.
Help appreciated I have this same issue - I want users to input data, which then uses a Match function to find the answer - depending on what this is, the colour changes.
I tested yours in 2013 version and it reacts the same way as you mention. When the range onscreen has to be redrawn, the CF is re-evaluated - you'll see the same behaviour if you simply scroll up and down on Sheet1 so that the range is off- then on-screen again.
If I change the value of the control cell then the cells on sheet 1 do not change their formatting.
If I switch to sheet 2 then the sheet 2 range has changed there formatting (based on the control cell in sheet1).
Sometimes, you may remove the check mark of the Preserve cell formatting on update item in the pivot table options accidentally.
And in this case, the formatting will be removed after refreshing if your pivot table contains cell formatting.