Something sounds wrong in your description.
Disabling the System - Admin Tools plugin cannot have an effect on crawling images. At least not for a crawler running on your site.
Replacing the .htaccess Maker-generated .htaccess file with the Joomla defaults can, indeed, have an effect on this, depending on what exactly you mean with "indexing the images for the image sitemap". If they are trying to crawl your site to find image links (is this 1998 all over again?!) it might get blocked by the "Block access from specific user agents" feature.
Nicholas K. Dionysopoulos
Lead Developer and Director
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Please keep in mind my timezone and cultural differences when reading my replies. Thank you!