I suspect the issue is due to the way that ACF instantiates the WP tinymce. Due to the requirements of the repeater and flexible content field, the WYSIWYG field must be duplicate-able at run time, which the default WP WYSIWYG does not offer.
I have a feeling that if install and use the WP WYSIWYG field (add-on) your shortcode button will work as expected. If not, the issue most likely lies within the shortcode plugin as it expects only 1 wysiwyg on the page.
Try out the add-on but be aware it won’t work within a repeater / flexible content field.
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