Jack seemed to have almost no misgivings or suspicions about Ianto during the stopwatch scene
What I can tell you without having to rewatch is that it's always been my impression that Jack had no misgivings about trusting Ianto from the moment the nods were exchanged at the end of Cyberwoman. I have NO IDEA what may have happened between Lisa's death and the nods, but I'm convinced there are no trust issues between Ianto and Jack from Small Worlds onwards. (Yes, I think sex was involved somehow, but my mind goes to pretty filthy places whenever I try to figure out how.)