I tried the free version and it found 500 pages with 18 page breaks.  I bought it thinking I had more pages to index and now it is only indexing/finding  3 pages and is giving me an unkown error when I goto the site map location.  It "lost" or can not find all the pages now since I installed the program... I even tried to go back to the free version and now the free version is finding only three.... what did the program do to make those pages disappear from the site map?  I am lost....  I need to figure this out or take this down off my site IMEDIATELY.  Please let me know what has happened.

I work with a magento template.  website:  [ External links are visible to forum administrators only ]

Great...... I took this off my site and tried to run the free version again and now that the program is off the root ...  it still only see's 3 pages.  ....  seriously NOT GOOD. What did the program do to my site?   Now the site will not index at all.... 
Hello,

sitemap generator doesn't (and cannot) affect your website - it's installed in a separate folder and works independently.
Please PM me your generator URL to check this further.
Thanks for getting back.  I installed it again I beleive that the site has limits on how many times it will run a crawler on the site somehow and that was the reason because when I tried again the next day it worked fine... EXCEPT....  it is now giving me a "fatal error" :

Fatal error: Allowed memory size of 268435456 bytes exhausted (tried to allocate 46412923 bytes) in /home/mxangels/public_html/generator/pages/class.utils.inc.php on line 102

Website:  [ External links are visible to forum administrators only ] 

The generator should be able to be reached at:  [ External links are visible to forum administrators only ]
"I've updated your crawler settings, please check now."

I've been having the exact same issue. Can you post how you changed her crawler settings, so I might be able to troubleshoot from information found in this forum?
I'm having exactly the same issue here.  Can someone please help?

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I continue to have this problem.  I've tried the suggestion of adding www to the start URL and still nothing.  Why does this continue to be an issue?

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Hello,

links in navigation menu are handled with javascript:
<a title="Moldova" onclick="window.open('http://domain.net/html/programs.php?program_name=moldova','_self')" href="javascript:void(0);">

you need to have the lin kin href attribute to make it crawlable:
<a title="Moldova" onclick="window.open('http://domain.net/html/programs.php?program_name=moldova','_self')" href="http://domain.net/html/programs.php?program_name=moldova">
Per your suggestion, I converted all the links to straight HREF tags (no javascript) and still come up with the same problem.  No entries generated in my sitemap.

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I deleted the configuration file and started over and now it seems to work.