It's been reported that this problem happens if you delete any of the standard categories and you've used up the total number of categories (15) to the point that adding back any of the deleted categories would cause the count to exceed 15.
When you reinitialize the Palm with a hard reset, it sets up all the standard categories, but they look newer than the categories on your desktop. That causes the built-in applications conduits to think that the categories on the new pristine Palm are the correct ones, so it stomps out your desktop categories! The workaround...