The former Yeovil chief suffered his second successive defeat since taking charge against in-form Southend.
Brighton let in a late winner at relegation rivals Leyton Orient on Saturday. They conceded twice in the closing stages this time to slump to an eighth league defeat out of ten at home.
Southend were the better side in the first half and deservedly went ahead in the 23rd minute.
A cross shot from Alan McCormack was pawed away by keeper Mikkel Andersen, making his home debut for Brighton on loan from Reading.
Theo Robinson then fed the ball back across the face of goal for Lee Barnard to slot his sixth goal of the season and first since October.
It could have been worse for Brighton a few minutes later, Robinson volleying over from a chip forward by Anthony Grant.
They capitalized on that let-off to level just before the break through another of their five home debutants.
Lloyd Owusu, borrowed from Cheltenham, thumped in a header from a cross by fellow loanee Gary Borrowdale.
Brighton looked the more likely winners after that and French winger Seb Carole hit a post early in the second half.
But their habit of letting in late goals came back to haunt them again as Barnard curled in a beauty from outside the box with five minutes to go.
Robinson, on loan from Watford, converted Kevin Betsy's cross from close range a minute from time to make certain of Southend's seventh win out of nine and maintain their slim hopes of a play-off place.