Changes to Rhino tolerance have no effect until components are re-triggered. Reconnecting an input does that, so does closing and re-opening Rhino - but that takes longer.
I think it’s significant that the invalid surface fragment (when there is only one) is near the seam (start / end point). There may be some things you are doing that don’t guarantee the correct sequence of points (for IntCrv) or curves (for Loft). Keep the code clean!
And always post a GH file when you start a thread. 