First off, great plugin. I spotted it a few months back and it looks impressive :)
I'm the author of Meta Slider. One of our users has discovered a problem. When SEO Slides is activated, Meta Slider lists all of the available media files as slides on every slideshow (in the back end).
I've tracked this down to line 1909 of SEOSlides_Core.php - hide_imports() function.
The pre_get_posts filter is being applied even on the Meta Slider admin page, the tax_query is overriding the tax_query that meta slider uses to populate the slides.
I haven't investigated too much, but if this filter is only needed on the SEO Slides admin page, please could you check the current page before adding the filter?