This is probably minor but I can't figure it out. After we did a backup and restored into a different directory everything seems to work with the exception of the search.
Originally we thought this was an issue with the search plugin we were using but we deactivated it and deleted it and the problem is still there with the standard WP search which we have in one of the sidebars.
The problem is that when we do a search the first page of results displays correctly but when we click on the link to retrieve the next page it displays the home page due to some redirect issue.
First page of results shows as this:
http://oursite.com/?s=news and returns the results correctly
clicking on the retrieval of the second page of results shows this:
http://oursite.com/page/2/?s=news but displays the home page of the site.
(note I just changed our actual domain name to oursite)
The search works correctly on the original site. So I think that after the restore into a different directory some path is not set correctly.
Also noticed one other thing. Once the backup is restored all the links in pages and posts are changed correctly to reflect the new domain. However we have some links embedded in footer.php that are not changed. I don't know if this is by design or something that should be changed. Its not a big deal we can go in and change these manually if necessary.