Measure Group with Two Partitions

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We have a cube which currently reads data from two separate partitions for the same measure group. By separate partitions, I mean coming from different tables. Then we have scope statements, which decides at which hierarchy level, what we show in our cube...i.e at certain level, cube shows numbers from Table_1 and at higher levels, cube shows numbers from Table_B. What is going on is, when I process both partitions at the same time, I get correct numbers. However when I process one after another , some numbers are doubling . Any reason what maybe going on? I have checked the source queries and they look good. Thanks

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