I'm having the same problem as baggins999 in the thread, http://wordpress.org/support/topic/35-select-all-doesnt-select-in-update-plugins-area?replies=6
I'm reposting here, after being told to start a new topic.
As baggins999 said: On the WordPress Updates page, in the plugins section, the "Select All" button doesn't do anything.
Ordinarily, I use desktop software to manage all of my updates, and that's working fine for the WP and theme updates, but not the plugins. (That has nothing to do with my desktop software. It's a problem since I updated to WP 3.5.)
So, I'm now updating plugins manually, but the "Select All" button doesn't work manually, either. (Ditto the "select all" box on the Installed Plugins page.)
This means clicking each plugin, individually, on the updates page. I did it yesterday, for the plugins that were updated quickly once 3.5 was released. Now, I'm going through the process again -- still updating plugins manually, one-by-one -- for this morning's Akismet update, plus a few other plugins.
esmi had posted a list of suggestions. So far, none of them have helped:
I deactivated all plugins (had to click each manually, one by one, since the "select all" option stopped working on the Installed Plugins page, as well).
That didn't solve the problem.
With the plugins still deactivated, I switched to the Twenty Eleven theme (manually updated), and that didn't help either.
This is going on, on all of my websites, regardless of themes or plugins used.
On esmi's lists of fixes, manually resetting the plugins folder might be my next step, but I don't have much hope for that. Frankly, I'm mot sure that this is worth the trouble.
The remaining solution, re-uploading all non-WP-content files & folders from a fresh WP download, for about 50 websites would be far too time-consuming, especially during the busy holiday season.
Unless 3.5 resolved major security issues, I'm sorry that I updated. I may revert (from site backups) to the previous WP version. Reverting with one click works, for now, but I'm hoping for a better answer, soon.