Rumours surfaced claiming that the pair had ended their relationship and that the former Coronation Street actress was planning to move out of their Cheshire home.
"We clash and have ups and downs, like most couples," Flanagan told Star magazine.
"People hear about it because we're in the limelight. It's my private business, but we haven't split. We're still living together too."
The couple moved into the Cheshire mansion when Sinclair signed for Manchester City from Swansea City last summer.