You really should be making a child theme so that you can make your custom changes but are still able to update the main theme to get all changes that may be tied to the core. Much safer and easier.
So – before going any further with this one please take a look at the change document for 5.5.4 (and you may want to look at previous ones as well) and look at the changes to checkboxes and radio buttons. This may not fix the issue but I think adding this CSS and turning the ‘pretty’ checkboxes off at the top of the theme spFunctions.php file (if defined on your old theme) is the first place to start.
https://simple-press.com/documentation/codex/installation/changes/theme-and-templates-5-5-4/