This applies to version 1.9 Beta3 as of today and has been reproduced on a test system with no custom patches.
As it alters grades and makes entries that can only be eliminated with database commands, I list it as a blocker.
I can reproduce it by:
Import a single element from another course (say an assignment)
Go into "Categories and Items" in the gradebook, and now every assignment from the source course appears as a phantom grade item in the course receiving the import. There is no link to an original assignment in either course.
In the database, new items are added to the grade_items table for each of these entries. The value of iteminstance is NULL but itemmodule entries are not NULL.
The only fix for now is to delete these items from the grade_items table; they cannot be deleted from within Moodle.
I will confirm this on a fresh database when time permits.