• Fleck (pictured) shares an agent with Wilson
It was reported recently that both Fleck and fellow youngster Danny Wilson had rejected new deals with the Scottish champions.
At the time, Walter Smith expressed concerns that the pair, both 18, were putting the prospect of lucrative moves to England before their careers.
However, the Rangers boss has revealed that Fleck was unaware negotiations were even taking place on his behalf and has now instructed his representative to resume talks.
Smith said: "The players have the same agent and we have found out in John's case that there has been a slight misunderstanding between the representative and the club.
"John wasn't fully aware his agent was negotiating a contract and the negative press was a little hard on him.
"It was reported he had turned down the contract when he actually hadn't, so negotiations are now taking place."
Speaking on Blues News, Smith added: "Danny's situation remains the same but John is getting an opportunity to play and we are delighted with him, so hopefully something can happen."
Meanwhile, Jerome Rothen has claimed his ill-fated loan spell at Rangers was the result of comments he made about Paris St Germain directors Sebastien Bazin and Alain Roche in a newspaper interview last June.
He has been back in France recovering from swine flu and has not featured for the Ibrox side since the 4-1 defeat to Unirea Urziceni in October.
Rothen is now set to join Turkish side Ankaragucu until the end of the season.
He told the Daily Record: "Sometimes, I've learned, it's better to keep your mouth shut.
"But after I said my piece it would have served no purpose for me to stay at PSG. I would have spent the season playing in the amateur league.
"I made the choice to go to Glasgow but in reflection it wasn't a good choice.
"This winter PSG made it indirectly clear to me I couldn't go back so I've found a solution until the end of the season."