Have you tried to open and re-save a slave site in JMS manage site.
This should recompute stuff required for the single sign-in.

it gives this error when i try it:

Error writing configuration file [/home/masterdatabase/public_html/multisites/subdomain/configuration.php]

ok it is a permission issue as u said. but resaving didn't solve the problem..

This is normal as I have replied by email that your MySQL user does not allow "SHOW VIEWS" that allow JMS compute the cookie domain that is saved in the master index each time you save a slave site.
I have given to you the solution to add the cookie value in the master index once it is created.

I repeat that each time you change anything in JMS, this rebuild the master index and therefore your temporary fix will be lost.
This temporary fix is while you fix the permission of your MySQL user.

As I have replied to you by email, when you go in JMS tools and that you put your cursor over a table that is marked as a link, you must see the first tables that is referenced.
So if you see only "shared table" without any name, this mean that the privileges of your MySQL user is not enough.

If you have a root MySQL User, you can use PHPMyAdmin to see the privileges of the MySQL user and fix the permission issue.

what is "root" MySQL User?? i have a reseller account but i could not check the privileges and fix it..

i sent a mail to the hosting company but i am not sure that they will help..

In the meantime, have you put the cookie_domains value in the master index.
When you have posted your message that say that it does not works, the value was NOT present.