I have spent some time converting my files over to mod-rewrite. On some of my sections, there are tens of thousands of pages. I have made sitemaps to make this content easier for google to find. However, I seem to hit a ceiling of pages that google can index for each section.

Each section is a different subdomain so it is easy for me to check site:subdomain.mysite.com. But whether a section has 12,000 or 70,000 pages available, only about 6,000 pages get indexed from that section max. Ive left the sections alone for a few months to see if the amount would go up, but it stays about the same.

Has anyone else experienced this? Any ideas on how to improve it?