This time around though Gillingham had the skills of Manchester United loanee striker Febian Brandy, who looks a decent signing on this showing.
Even so, the now administration free Southend had chances to take the lead, the best falling to Dougie Freedman, who headed over the bar after former Blues keeper Simon Royce pushed up a James Walker shot into his path.
Then came the home sides turn. The referee decided that Simon Francis had pushed Brandy in the box but the travelling faithful saw a first, a Mildenhall penalty save! Big Steve diving to his left to push Simeon Jackson's spot-kick wide.
Would have had one of those against Brentford because sadly this one wasn't going to count, after Barcham had blazed the ball over the Blues crossbar, Gillingham took control of the tie with two goals in three minutes.
First, on 25 minutes, it was Curtis Brandy, playing a nice one-two with Brandy, placed the ball over the advancing Mildenhall.
Three minutes late, Fabian Brandy himself got on in the act, shooting low from the left past the Shrimpers keeper.
Any thoughts of a comeback probably ended when just after the half hour when Johnny Herd limped off and Anthony Grant went to left back with Jean-Francois Christophe going to centre-half, leaving Damien Scannell to try and cause some damage down the left wing, the Moose moving into his favoured centre.
However, it was to be ex-Blues midfielder Mark Bentley who was to confirm the end of Southend's cup dreams for another season, heading the ball home of the left-hand post in the 62nd minute.
Now it was a case of seeing the last half hour out without seeing any more damage, meaning injuries to players than further Gills goals, and at least that was achieved.
There was even the sight of Dougie missing another sitter, this time a real open goal, as a deflected shot from Walker fell to his feet but somehow he placed the ball wide.
Roycey also had to make a good save from a Christophe header, and there was a cheer when youth player Kyle Asante made his first team debut as a sub for Walker, yet most supporting Shrimpers were happy to hear the final whistle and head home with a club still to cheer on next week at Yeovil.
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