His remarks, made during an edition of the Mock The Week TV programme, were ruled to be offensive but no further action was taken, which prompted her agent to complain about the "slap on the wrist" when Adlington had been humiliated.
Boyle returned to Channel 4 - the official Paralympics broadcaster - earlier this week with The Boyle Variety Performance. A previous series for the station, Tramadol Nights, prompted more than 500 complaints after he mocked Katie Price's disabled son.
His tweets on Thursday night also targeted the Queen who declared the Games open during the ceremony at the Olympic Stadium in east London. "The Queen hasn't cracked a smile since Diana died," he said.
In another message he said: "I'd love to have the skill and dedication of some of these Paralympians, almost as much as I'd like to have their meds."
Many Twitter users condemned his comments. One praised Channel 4 for its coverage but said: "Shame you have idiots like Frankie Boyle undermining it with tweets poking fun."