Lengthy title lends a lengthy reply, but it’s actually a quite simple fix. First some background information on my process that lead to the issue:

1. Exported respective database tables from multisite install.
2. Renamed table prefixes (e.g. from wp_7_ to wp_).
3. Installed a fresh copy of WordPress (same version as multisite install) at new webspace.
4. Copied theme, plugins and respective blog.dir to above webspace.
5. Imported the exported database tables from step 1.
6. Checked menu, widgets, theme options, plugins, etc to verify all matches existing multisite.

The issue happened when I imported the wp_options table. There is a row called wp_user_roles that contains permissions for each user level (Administrator, Contributor, etc). This field had been altered on the multisite install (could have been a plugin or part of the multisite install?) to remove update_plugins and install_plugins from the Administrators list of permissions. Since I am using a fresh copy of WordPress, I ramped up another fresh install of the same version of WordPress and copied the wp_user_roles over to the site that wasn’t allowing me to update/add plugins and voilà plugins were showing they needed to be updated and my missing “Add New” button on plugins page was back.

Here follows the default option_value for wp_user_roles for WordPress 3.4.1:

a:5:{s:13:”administrator”;a:2:{s:4:”name”;s:13:”Administrator”;s:12:”capabilities”;a:62:{s:13:”switch_themes”;b:1;s:11:”edit_themes”;b:1;s:16:”activate_plugins”;b:1;s:12:”edit_plugins”;b:1;s:10:”edit_users”;b:1;s:10:”edit_files”;b:1;s:14:”manage_options”;b:1;s:17:”moderate_comments”;b:1;s:17:”manage_categories”;b:1;s:12:”manage_links”;b:1;s:12:”upload_files”;b:1;s:6:”import”;b:1;s:15:”unfiltered_html”;b:1;s:10:”edit_posts”;b:1;s:17:”edit_others_posts”;b:1;s:20:”edit_published_posts”;b:1;s:13:”publish_posts”;b:1;s:10:”edit_pages”;b:1;s:4:”read”;b:1;s:8:”level_10″;b:1;s:7:”level_9″;b:1;s:7:”level_8″;b:1;s:7:”level_7″;b:1;s:7:”level_6″;b:1;s:7:”level_5″;b:1;s:7:”level_4″;b:1;s:7:”level_3″;b:1;s:7:”level_2″;b:1;s:7:”level_1″;b:1;s:7:”level_0″;b:1;s:17:”edit_others_pages”;b:1;s:20:”edit_published_pages”;b:1;s:13:”publish_pages”;b:1;s:12:”delete_pages”;b:1;s:19:”delete_others_pages”;b:1;s:22:”delete_published_pages”;b:1;s:12:”delete_posts”;b:1;s:19:”delete_others_posts”;b:1;s:22:”delete_published_posts”;b:1;s:20:”delete_private_posts”;b:1;s:18:”edit_private_posts”;b:1;s:18:”read_private_posts”;b:1;s:20:”delete_private_pages”;b:1;s:18:”edit_private_pages”;b:1;s:18:”read_private_pages”;b:1;s:12:”delete_users”;b:1;s:12:”create_users”;b:1;s:17:”unfiltered_upload”;b:1;s:14:”edit_dashboard”;b:1;s:14:”update_plugins”;b:1;s:14:”delete_plugins”;b:1;s:15:”install_plugins”;b:1;s:13:”update_themes”;b:1;s:14:”install_themes”;b:1;s:11:”update_core”;b:1;s:10:”list_users”;b:1;s:12:”remove_users”;b:1;s:9:”add_users”;b:1;s:13:”promote_users”;b:1;s:18:”edit_theme_options”;b:1;s:13:”delete_themes”;b:1;s:6:”export”;b:1;}}s:6:”editor”;a:2:{s:4:”name”;s:6:”Editor”;s:12:”capabilities”;a:34:{s:17:”moderate_comments”;b:1;s:17:”manage_categories”;b:1;s:12:”manage_links”;b:1;s:12:”upload_files”;b:1;s:15:”unfiltered_html”;b:1;s:10:”edit_posts”;b:1;s:17:”edit_others_posts”;b:1;s:20:”edit_published_posts”;b:1;s:13:”publish_posts”;b:1;s:10:”edit_pages”;b:1;s:4:”read”;b:1;s:7:”level_7″;b:1;s:7:”level_6″;b:1;s:7:”level_5″;b:1;s:7:”level_4″;b:1;s:7:”level_3″;b:1;s:7:”level_2″;b:1;s:7:”level_1″;b:1;s:7:”level_0″;b:1;s:17:”edit_others_pages”;b:1;s:20:”edit_published_pages”;b:1;s:13:”publish_pages”;b:1;s:12:”delete_pages”;b:1;s:19:”delete_others_pages”;b:1;s:22:”delete_published_pages”;b:1;s:12:”delete_posts”;b:1;s:19:”delete_others_posts”;b:1;s:22:”delete_published_posts”;b:1;s:20:”delete_private_posts”;b:1;s:18:”edit_private_posts”;b:1;s:18:”read_private_posts”;b:1;s:20:”delete_private_pages”;b:1;s:18:”edit_private_pages”;b:1;s:18:”read_private_pages”;b:1;}}s:6:”author”;a:2:{s:4:”name”;s:6:”Author”;s:12:”capabilities”;a:10:{s:12:”upload_files”;b:1;s:10:”edit_posts”;b:1;s:20:”edit_published_posts”;b:1;s:13:”publish_posts”;b:1;s:4:”read”;b:1;s:7:”level_2″;b:1;s:7:”level_1″;b:1;s:7:”level_0″;b:1;s:12:”delete_posts”;b:1;s:22:”delete_published_posts”;b:1;}}s:11:”contributor”;a:2:{s:4:”name”;s:11:”Contributor”;s:12:”capabilities”;a:5:{s:10:”edit_posts”;b:1;s:4:”read”;b:1;s:7:”level_1″;b:1;s:7:”level_0″;b:1;s:12:”delete_posts”;b:1;}}s:10:”subscriber”;a:2:{s:4:”name”;s:10:”Subscriber”;s:12:”capabilities”;a:2:{s:4:”read”;b:1;s:7:”level_0″;b:1;}}}