That basically means that while permissions on objects that you have applied the tool to look like they have changed to what you asked them to be set to, that isn't necessarily the case. There's not really any easy way to find out if it has actually worked or if it has failed to function properly. The permissions will appear to you as if the operation completed successfully, whether it actually did or not, but when objects are then passed to others, they return to their previous permissions.
Unfortunately, there's levels and levels (and layers and abstractions and references) to the grid inventory and asset systems, and it isn't always clear that things have updated correctly end-to-end. (This is also one of the problems behind so-called prim-drift. Your viewer tells you that it has moved a prim from one place to another, but the server itself may not be told. Everything looks right to you, but it isn't always)
A prototype patch for the bulk permissions problem has been created and applied to the Snowglobe viewer (1.0.3-2537) for testing. Although, even if that appears to fix the problem successfully, we're not certain how long it will take Linden Lab to push a corrected official viewer out to the general user population.
In the meantime, we're inclined to echo Linden Lab's advice and suggest that you give the bulk permissions editor a miss until the problems are sorted out.
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