I had this issue the other day, make sure your vertices are all welded. I had a lone vertex hanging out in the middle of an edge and it was messing my swift loop up.
As far as I know, loops don't work if you don't have continuous quads. That's kinda the point of loops. On both sides of your problem you have polygons, it only works on quads.
From Wikipedia, searching Edge loop (computer graphics) "In a stricter sense an edge loop is defined as set of edges where the loop follows the middle edge in every 'four way junction'. The loop will end when it encounters another type of junction (three or five way for example)."
Fast way to check overlapping faces is to ctrl+a to select all vertices and then weld them with a threshold on 0,01 and if its a change in the before and after number you got overlapping vertices.
When you converted the pentagons you have into quads, did you use any bridging? It may be a case that your edges are not connected but laying on top of each other. I would check this by smoothing it and seeing if the edge flow does anything unpredictable. If so, delete the face and then cap it instead of bridging.
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@Kbrom, yes this is what I thought also but I could not find overlapping vertices. Is there a fast way to check ?
From Wikipedia, searching Edge loop (computer graphics) "In a stricter sense an edge loop is defined as set of edges where the loop follows the middle edge in every 'four way junction'. The loop will end when it encounters another type of junction (three or five way for example)."
@Velktri, I had that problem before but luckily I am not that sloppy anymore =P
Learning the most from making mistakes! ^^