I would suggest you check your masking options as it sounds like your segment 2 is overwriting your segment 1. Please read Segment editor — 3D Slicer documentation.
Your steps leading up to when it is not working for you would be helpful along with any screenshots. What type of volume is it? I can only think that you may be running into a limitation of using multi-volume rendering with the maximum intensity projection option instead of composite shading. See related post below: