In https://github.com/avstudnitz/AvS_FastSimpleImport/blob/master/src/app/code/community/AvS/FastSimpleImport/Model/Import/Entity/Category.php#L477 you are setting the category position to 10000 when it is not specified.

I am currently tracking an issue that apparently relates to this.

The symptoms are, after an import whenever I rearrange a category within its parent the new position gets set to 10001, sending it to the bottom.

Afterwards whenever I rearrange another category in the same parent, the first category gets reverted back to 10000 and the new category gets assigned to 10001.

This is because of the logic inside Mage_Catalog_Model_Resource_Category::_processPositions

I am unsure about how best to approach this issue. Suggestions?