I think that sentence's order is swapped. The clause with the past perfect tense is suppose to occur first, then the other clause. So according to your sentence, you didn't clean your desk FIRST, then you became busy.
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RoroBecause I was/had been so busy, I hadn't cleaned my desk for two weeks. ?????????????????????????????????????????? [A husband -- to his wife, cleaning his room] .... Where is that important number I wrote on the dust!?