heres another thing you can do with illy files in flexi...
when i get a drawn file with "strokes" put on them and i need to work on them i FIRST get rid of all the "strokes" [they can all be replaced if needed] copy paste a reference and dont mess with that one.
they will come apart,,anything will come apart ,,convert to outlines ..ungroup all,uncompound all....delete the inner and outer line
now you have one vector line to build from,,,apply inline,outline ,contour cut from flexi off that line.
on the deal you asked about where it was putting a contour inside and ouside ..that line or "stroke" needs uncompounded..then you can select just one of them for applying contour cut. now if there are centers as in o's ,etc..you will have to go select them along with outers,compound just them together.
remember no matter what program your using..ungrouping and uncompounding are two complete different tools.this is probly one of the first things that need addressed to learning vector
hope this helps someone