This can occur with any combination of LaserWriter 8.4.x and ATM 4.0 when setting up a printer for the first time. Once a LaserWriter has gone through Setup in Chooser, successive Setups of that printer work properly.
This issue should be resolved in a future version of the LaserWriter driver software. Until then, you can use one of the workarounds listed below.
Workarounds
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Disable ATM 4.0 before setting up a LaserWriter for the first time in Chooser.
Use the LaserWriter 8.3.4 software. Versions of the LaserWriter driver earlier than 8.4 do not exhibit this issue.
Use LaserWriter 8.4.2. Although susceptible to this issue, results are better when using the LaserWriter 8.4.2 with ATM 4.0 software.