Okay so here is my issue and I'll try my best to expalin it.

I have created my site map through site map admin and it creates the three site maps for the index, categories and products. However it displays:

Generated Google Sitemap Index Successfully - http://www.mydomain.com/sitemapindex.xml

The above message is displayed for all three files but the problem is that they are really not there and were actually created in the http://www.mydomain.com/mystore/ directory which is the correct place.

And eventhough sitemapindex.xml, sitemapcategories.xml and sitemapproducts.xml are all in http://www.mydomain.com/mystore/ - sitemapindex.xml has the path of the other two files as http://www.mydomain.com/sitemapcategories.xml and http://www.mydomain.com/sitemapproducts.xml

And if I hit send to crawler in step 2 of site map admin, it sends the sitemap path of http://www.mydomain.com/sitemapindex.xml

So this is causing the search engines to fail when they try and crawl my site.

Any ideas on how to fix? Thanks.