I enabled domain mapping on my wordpress multi site, but issue is blogs with the mapped domain does

Hi,
I installed Multi domain and the domain mapping plugins.

Multi-domain plugin seems to works beautifully.
So I have couple off site setup currently using the multidomain plugin.

Example:
http://Site1.edu/
http://Site1.edu/Blog1/
http://Site1.edu/Blog2/

http://Site2.edu/Blog1/
http://Site2.edu/Blog2/

No I installed the domain mapping plugin and mapped
http://Site2.edu/ to http://Site2.edu/Blog1/

Which seems to work.
Problem is when ever I go to the dashboard of http://Site2.edu/Blog2/
i.e. http://Site2.edu/Blog2/wp-admin/
and add posts, it makes changes to the http://Site2.edu/ site.

any idea why?

Thanks
Manoj