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I just ran into this issue while working on a module that creates its own fields.
I was testing the module by adding new fields through the fields ui but the fields were not being saved. I couldn't figure out why until I realized that an error message was being output but it was being added to the "message okay" box instead of the "message error" box.
It looks like the errors being output through drupal_set_message should have a $type property added.