Magento

I tested this several times by installing the store on for separate sites.  Everything works fine until I use store connector to install something, after lets say the modern template is installed, the navigation links in the admin no longer work, the calender pop up to selects dates no longer works, in the categories manager, you no longer can see your list of categories. 

so like I said,, everything is ok until the template is installed.  this doesn’t make sense, the template shouldn’t change anything in the admin.

let me know your thoughts on this issue

You need to go in and change the file permissions in the JS folder. That should solve this problem.

There is a fix for this. For some reason it changes permissions. check out this thread for the solution.
http://www.magentocommerce.com/boards/viewthread/17457/#