Not sure you have the right plugin you are talking about. All it does is embed an image and has no bearing at all on what theme is active. It literately uses HTML to display the image.
Below is exact code that it displays.
<img width="134" height="69" src="PATH_TO_IMAGE_HERE" alt="Secure Site Seal">
It is IMPOSSIBLE to cause “numerous errors and compatibility issues” as you say.
If you are using SSL embed code from your provider, you are probably pasting it in wrong. Would gladly help you figure it out.
Please let us know what the issue is you are having and we will fix it for you.
There is no plugin settings page for this. Once you activate it, it adds a function to your site that speeds it up. Please explain what you mean by “Cant see it in plugins or anywhere?”