/wordpress being added to homepage url + permalinks problem

I migrated a site from a sandbox where wordpress was installed in the root, to a live site where wordpress was installed in a subfolder. this caused problems, so I copied wordpress out to the root of the live site and re-imported the site from the sandbox. everything is working fine now with two exceptions:

(1) The home page url has “/wordpress” added to the end automatically and is still pulling this page from the live site subfolder (it breaks when the subfolder is renamed). All other pages don’t have this added to the url & work fine when the subfolder is renamed. The permalink for the home page does not include /wordpress, btw.

(2) I can’t change the permalinks to a custom structure, have tried several times and it won’t save.

thanks for any help!