Have you used the "Reschedule Uncompleted Work" tool in the Tracking menu to
move those task up to the date when you think they'll be able to start or
are they still sitting back there on the dates where they were originally
scheduled? Project don't really know much about the current date. If we
have a 1-day task originally scheduled for last Monday with a deadline of
last Wednesday sitting in the schedule, if it still shows on Monday the
missed deadline indicator doesn't light up even if the task is not marked as
complete. Only when the task gets moved - pushed by a predecessor or by
rescheduling so it falls in the schedule on a date later than the deadline
date does the indicator turn on. The current date doesn't enter into it at
all.