upgrade and installation problems

I am at a loss. I have been running wordpress flawlessly for about three years now with no problem. Lately when I upgraded my installation I notived that my plugins were not activated. When I tried to activate them, i was told that they were activated but they were still listed as unactivated. After much searching and not finding a solution I tried a couple of other things. I installed a widget too see if that was working and after installation, the board no longer functioned. I had to edit a few lines out of the widgets.php file. They were:
if ( empty($wp_registered_sidebars[$index]) || !array_key_exists($index, $sidebars_widgets)

and:

unset($sidebars_widgets[‘array_version’]);

I am not php savvy, but this at least allowed me to get the board back to a “readable” state.

My next thought was to try a “clean” install in a different virtual domain.
I created a new database (empty) and installed wordpress fresh into my personal domain. After install I ran wp-admin/install.php and it seemed to go fine. It presented me with my password and when I went to log in I got this error:

Warning: Invalid argument supplied for foreach() in /var/www/bobtongue.com/htdocs/wordpress/wp-includes/capabilities.php on line 31

Warning: Cannot modify header information – headers already sent by (output started at /var/www/bobtongue.com/htdocs/wordpress/wp-includes/capabilities.php:31) in /var/www/bobtongue.com/htdocs/wordpress/wp-includes/pluggable.php on line 595

Warning: Cannot modify header information – headers already sent by (output started at /var/www/bobtongue.com/htdocs/wordpress/wp-includes/capabilities.php:31) in /var/www/bobtongue.com/htdocs/wordpress/wp-includes/pluggable.php on line 596

Warning: Cannot modify header information – headers already sent by (output started at /var/www/bobtongue.com/htdocs/wordpress/wp-includes/capabilities.php:31) in /var/www/bobtongue.com/htdocs/wordpress/wp-includes/pluggable.php on line 597

Warning: Cannot modify header information – headers already sent by (output started at /var/www/bobtongue.com/htdocs/wordpress/wp-includes/capabilities.php:31) in /var/www/bobtongue.com/htdocs/wordpress/wp-includes/pluggable.php on line 770

I have searched in vain for a solution. I could not find any broken lines in my user_roles database entry and magic quotes in all flavors is turned off via the php.ini file. I have verified this. I am at a loss. Any help would be appreciated. I am running wordpress 2.6.2 on gentoo linux 2.6 kernel php version 5.2.6-r7 and apache 2.2.9-r1.