Вы делаете суммы в подзапросе, который наиболее вероятно выполняется один раз для каждой строки во внешней таблице.
Вместо этого попробуйте использовать оконную функцию:
SELECT Season,
CustomerCode, Customer,
VarietyCode, Variety,
GrowingMethodCode, ProductSizeCode, PackType, Market, Brand,
WeekNum, Qty_Planned,
SUM(Qty_Planned) OVER(PARTITION BY Season, CustomerCode, VarietyCode, GrowingMethodCode, ProductSizeCode, PackType, Market, Brand ORDER BY WeekNum) AS Qty_Planned_Running,
SUM(Qty_Shipped) OVER(PARTITION BY Season, CustomerCode, VarietyCode, GrowingMethodCode, ProductSizeCode, PackType, Market, Brand ORDER BY WeekNum) AS Qty_Shipped_Running
FROM [DataMiningImports].[Apples_Planned_vs_Shipped]
ORDER BY WeekNum