So i looked around in My Paratext 9 folders and found a custom.sty in my project but looking at what was in it, it doesn’t seem to like it would be causing the issues I’m having.
Here is what was in it:
Custom style file created by the upgrade to Paratext 8.0. It is based upon
the original style files used by your project.
These files have been removed, but a backup of the files has been saved to
usfm.sty.bak and custom.sty.bak.
\Marker toc1
\OccursUnder h h1 h2 h3
\Marker toc2
\OccursUnder h h1 h2 h3
\Marker toc3
\OccursUnder h h1 h2 h3