With Martinez's move to the JJB Stadium on hold following a misunderstanding over compensation for his assistant Graeme Jones and chief scout Kevin Reeves, rumours were rife that the 35-year-old could be having second thoughts.
But Jenkins, who spoke to Martinez after the press conference to unveil him as Wigan's manager was cancelled, was quick to dismiss such suggestions.
"I think the fact a couple of things were not sorted out is irrelevant to Roberto leaving our club," Jenkins told the South Wales Echo. "He has made his thoughts clear - he was in Wigan at the press conference to unveil him as their new manager.
"The issue is that we want fair compensation for two employees that we have invested a lot of time and money in. I have spoken to Roberto and he understands that.
"It hasn't changed my rapport with him. This was not about Roberto and Swansea, it is an issue we have with Wigan."