The Cobblers, who played more than an hour with 10 men after having Chris Hackett sent off, wasted a great chance to open the scoring after just eight minutes when former Shrimpers loanee Roy O'Donovan saw his spot-kick saved by Bentley who dived well to his left to parry the shot to safety.
To add to Northampton's frustration, Hackett was dismissed in the 22nd minute after being shown a second caution for a late challenge on Straker.
Having found themselves 2-0 down Corr and Atkinson were both denied by Duke late on but Northampton boss Aidy Boothroyd could not hide his disappointment at the final whistle.
"It's a very poor result and I thought we'd come and get something here with the players we've got coming back," said Boothroyd.
"Roy O'Donovan will score plenty of goals for us this season and I'm not going to point any fingers at anyone for missing penalties.
"But if that goes in we're 1-0 up away from home we can then manage the game from there.
"Then came the red card and while Chris Hackett is a terrific player for us he was very naive."