When you publish a theme you will hit cache issues initially as the theme is newly being served.
Unpublished themes have redirects and other cruft added to the them.
Either compare results only from when each theme is live after a short time after making initial requests,
or use results from when they are both unpublished.
Also the nature of the internet is asynchronous, more so when javascript is being used.
So if your focusing only liquid disable javascript.