Harriers switched back to their trusty 3-5-2 formation after an unsuccessful attempt to play 4-4-2 in Saturday's Scunthorpe defeat.
Adie Smith moved over to the right side of midfield with Hinton, Scott and Morgan making up the back three.
But what ensued was a scrappy opening with no chances and little good football.
Southend wide mman Clark rose to head aimlessly over the bar on three minutes but otherwise there were no shots at goal.
Harriers often had just the better of the play but could do little to trouble visiting keeper Flahavan despite a few goalmouth scrambles.
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