When editing categories the portlet changes the vocabulary to the 1st one. I've seen twice the vocabulary combo to change just after clicking the OK button. Parent category remains good, in the table, but those categories disappear in the editing portlet because they belong to another vocabulary.
When editing categories the left and rigth categoryId fields gets confused.
The Asset publisher does not check the vocabularyId of the selected categories, so if the left-rightCategoryId match the selection, even if not in the same vocabulary, the asset publisher shows them.
The workaround is to check every vocabulary has it's own left-rightategoryId scope. Another workaround is to create a portlet to fix the left-rigthcategoryIds and to fix the vocabularyId to the rigth one.
The left-rigthcategoryId is simple to check, but it's a bit complicated to manage, because a category reorganization may require now to renumber the left-rightcategoryIds in all the categories.