DrupalDefaultEntityController::load() fails if query has more than one row with same "key", causing taxonomy load problem

My apologies if this is already in the issue queue -- many functions and systems seem to be involved so possibly this is filed under another category.

I noticed that the following use case with taxonomy "Apply To" types does not work and traced it back to the DrupalDefaultEntityController::load() function.

- latest head install (7.x-dev, sept. 3), clean install
- admin/structure/taxonomy/1
- Apply to content types: choose Article and Page
- Save
- Your selections are both in the database now (as we can see in table {taxonomy_vocabulary_node_type}).
- Only the Page type is visible in the table. (We expect both types to be visible), as they are both in the database.
- Edit the vocabulary again
- Notice that the Article type, previously selected, is not selected. We expect it selected because it is in the database.

Part of the problem seems to be that the TaxonomyVocabularyController's buildQuery() uses a join that causes the query to result in a number of rows with the same vid, differing only in the type column.

When the parent class's load() function is called, it uses the database's DatabaseStatementBase::fetchAllAssoc() function which attempts to return the association by key, and *only the last row* is used.

For example,

| vid | name         | ... | type     |
|   1 | Tags         | ... | article  |
|   1 | Tags         | ... | page     |
|   2 | Countries    | ... | article  |
|   2 | Countries    | ... | page     |
|   2 | Countries    | ... | type3    |

results in

array(
  '1' => array(
    ...
    type => 'page';
  )
  '2' => array(
    ...
    type => 'type3';
  )
);

within DatabaseStatementBase::fetchAllAssoc().

I've looked in the issue queue (including #460320: Standarized, pluggable entity loading (nodes, users, taxonomy, files, comments)), and I'm a bit stumped as to how to fix the problem, because I'm not sure which function is not doing what's expected/assumed.

(I'm at DrupalCon if anyone wants to discuss the problem)

Cheers,

Albert.