you can do it with applescript, if you have gui scripting (aka ui scripting) going.

some code:

with timeout of 1200 seconds
tell application "Acrobat 5.0" -- to set the open options
activate
end tell
tell application "System Events"
tell process "Acrobat 5.0"
tell menu bar 1 -- menu bar
tell menu "File" -- menu
tell menu item "Batch Processing" -- menu item
tell menu 1 -- sub-menu
delay 1
click menu item "3 Set Open wBookmarks" -- sub-menu item
end tell
end tell
end tell
end tell
end tell
end tell
end timeout

(i know my post isn't very timely, but i just saw the topic as i was searching for something)

hope this helps.