I don't know if this is related, but we have often experienced issues where some performance data (clicks, impressions) is present in the report at one time, but later runs of the same report do not include that performance data. So the clicks and impressions disappear. For us, it is not so much that the report is inconsistent with the AdWords UI (although that may be true as well -- we don't often compare them). It's that the reports don't stay consistent over time. I've always assumed that these disappearing records are due to Google's click fraud algorithms, where activity that initially gets into the report is later scrubbed when it was determined to be click fraud.
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