I think Ianto is generally wondering what exactly he means to Jack. All the issues that come with loving an immortal, on top of which Jack is not exactly great at communicating his feelings/commitment.

True - there plenty of other examples of Ianto being uncertain or insecure about where he stands with Jack. It's just that they usually don't involve Gwen. It is interesting that he doesn't seem to resent Gwen much if at all given that she is Jack's golden girl a lot of the time. By contrast, it cracks me up that Owen does resent Ianto's relationship with Jack.