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The series index is set according to the series tweak (series_index_auto_increment) if the series name changes in some way, including case changes.
Looking at the code, my guess is that in your odd cases the series name is changing to a name that already exists, which will cause the series index to be updated according to the tweak. My reading implies that the signal that triggers this update occurs after the downloaded index value is written into the series_index box, with the result that the downloaded value is replaced by the computed value.
I agree that this is not desired behavior. I suggest you file a bug report.
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