That's an interesting question Ade.
How are you are drawing the cross sections?
Cross sections should get drawn in sequence, according to the string label. So, for a set of sections starting with "D" say, the string names will normally start at D001, which will corrsepond to the first point on the reference string, and the number in the section string name will increase from there - so D002 for the second point on the reference string, and so on.
I would create a plan drawing, and draw on it the reference string, and the cross section strings. Annotate the cross section strings with the string name, then check that they increment as expected as you work your way up the reference string. I expect that you'll see an issue somewhere, and where it occurs might give you an idea as to why.
It might also be worth checking the reference string itself. I would create a GENIO file of it, then look for any negative X or Y coordinates, which would signify a gap. I would also use the Points option in Dynamic Reports to check the reference string, because it draws a marker at the point on the screen, to check that the sequence of points is as you would expect, and doesn't double back.
I'm assuming that you don't have a very long reference string - more than 46656 points - as this is the limit for the number of cross sections in a single section set.
Regards,
Jon