Brendan, who was partnered with celeb dancer Charlotte Hawkins, had rowed with Shirley over her comments and marks in this year's live shows.
Despite having been voted off the show, The Sun reported that Brendan was still annoyed at Shirley over her feedback.
And, apparently, getting the new judge job over him.
"Brendan is clearly very bitter about missing out on the role and hasn’t held back on taking out his anger on Shirley," a source accused. “He goes out of his way to ignore her backstage during show breaks and makes her feel very uncomfortable."
Speaking to The Sun newspaper this week, Shirley spoke out about the supposed feud.
She said of Brendan: “He’s confrontational. Every other professional was extremely respectful, very well-mannered, ‘How are you Mrs Ballas? You’re doing a good job’.
“I was quite surprised. I got my feelings hurt because when he was with Camilla (Dallerup) all those years ago they came to our home, had dinner. But again, in my industry I’m used to that. He’s going on chat shows saying I’m her equal and this, that and the other. I don’t need to put somebody else down to build myself up.”
New head judge Shirley told the tabloid she would accept an apology if it came her way - but wasn't going to make an effort herself.
“If he comes in my direction and he’s gracious and courteous . . . but I’m not going to run after him," she said.
Last month, Brendan played down the claims of a feud in an interview on ITV's Lorraine.
He explained: "[A newspaper] reported that I was hurling abuse over the balcony and I wasn't. If someone is undermarked we all go 'undermarked! Undermarked!'"
Brendan went on to say he didn't regret speaking up, explaining: "I tend to be more argumentative than the rest of the pros. The rest will be [in the change rooms yelling] left, right and centre, but I don't control myself for the change room I have to do it live on air.
"I'm a nice person - my wife will tell you. I don't hold back and morally I'm big on doing the right thing at the right time and I had to stick up for Charlotte from Shirley."
Strictly Come Dancing continues this Saturday night on BBC One.
The series will be concluding with its live grand final.