You are in "Easy mode" which hides 99% of all options:
http://www.microsystools.com/products/sitemap-generator/help/easy-sitemap-generator-mode/
You can read about "output filters" here:
http://www.microsystools.com/products/sitemap-generator/help/website-crawler-output-filters/
And about analysis/crawl filters here:
http://www.microsystools.com/products/sitemap-generator/help/website-crawler-scanner-filters/
Concerning 100 links. That is default for HTML sitemaps:
http://www.microsystools.com/products/sitemap-generator/help/create-html-sitemaps-tutorial/
http://www.microsystools.com/products/sitemap-generator/help/generate-website-html-sitemap/
25000 is default for XML sitemaps:
http://www.microsystools.com/products/sitemap-generator/help/xml-sitemap-generator-tutorial/
http://www.microsystools.com/products/sitemap-generator/help/xml-sitemaps-page-limit/
Anyways, it sounds like you are running in "Easy mode" and used on of the presets at some point. That explains most of the trouble you have had!

(e.g. A1SG would never include .jpg URLs in output unless some options been modified, e.g. through presets)
If you continue to have problems, please drop an email with your project file, and I will take a look
