It could be that the mod required template edits and you have not done them for your new style. It could also be that the mod has automatic template edits that won't work with your new style and you will have to manually do the template edit instead of using the plugin to do the template edit.
You should reread the instructions for your modifications and see if any have template edits you need to do. and, you should read the code for your modifications and see if there are any automatic template edits and then look at your custom style and see if it will work.
Reuploading the modification won't do anything for this problem.