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The causes for a machine not showing up vary somewhat.
By whatever method you prefer, get a list of the machines that aren't showing up in ePO, then you just need to find out what's different about those machines. :)
Are they listed at all in ePO?
Do they have an agent?
Any errors in status monitor?
Are they imaged machines? You could have duplicate GUIDs.
PS - or do you just mean that your discovery task is not querying the directory properly?