What version of SW are you using? If you're not using the most recent version, can you upgrade, or post the file here?
I remember SW previously had some bugs where the shell direction was displayed incorrectly, but I believe they've been fixed over the years.
If you're model is simple enough one possible fix is to alter the surfaces to represent the mid surface. This way the top/bottom direction definition won't matter.
I'm using SW2017 but I think it's still buggy with the shell preview feature. The previewed shell mesh thickness seems OK but I still really don't trust it.