I cannot recall if this applies to the MOBI format, but in some cases information for an ereader is based on the metadata that is inside the file. Also, not all ereaders make use of the information in the Series and Series_Index fields.
I've got no idea about the order. Well, ok, a completely wild guess that I doubt is likely: it's being sorted alphabetically by the textual name of the numbers: zero one, zero three, zero two.
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