Update: The pop is not heard when pressing the loop button manually, so this rules out that being the problem.
Stage traxx region markers generate small "pops" in the right speaker, I listened to my sample and it was clean without the markers, when listening to the same sample with markers (without the loop active) small "pops" appeared when passing through said markers. So I think it is a problem with the region markers. The "pop" problem is not when repeating a section, but when going through the markers. So if I have several multitracks with elements with a lot of attack this is not perceived, but when I have a single element with a constant sustain such as ambient pads, this "pop" is perceived.