Upgrading Drupal

I just installed 4.3 from fantastico and upgraded just as soon as I saw it was working properly. Can anyone give me a clue as to what this error message means?

warning: init_theme(): Failed opening '' for inclusion (include_path='.:/usr/lib/php:/usr/local/lib/php') in /home/seguin/public_html/cankor/includes/theme.inc on line 51.

warning: Cannot modify header information - headers already sent by (output started at /home/seguin/public_html/cankor/includes/common.inc:402) in /home/seguin/public_html/cankor/includes/common.inc on line 256.

A few days ago I tried to update my Drupal 4.3.2 to 4.4.0, I followed the instructions, but I got tons of errors afterwards, so I had to downgrade back to 4.3.2, but now I noticed that whenever I try to access the module section, I guest this error:
Fatal error: Cannot redeclare check_output() (previously declared in /home/chspower/public_html/ridd/includes/common.inc:667) in /home/ridd/public_html/ridd/modules/filter.module on line 143

Any thoughts on this? Any help would be greatly appreciated.
Thanks in advance

I'm running 4.3.2 on a hosted shared server to which I don't have root access. It was installed from within the Fantastico page on that server. If I FTP files to the server, they do not have the same permissions as teh current install. How can I upgrade this to 4.4.0:?

I have now upgraded to Drupal 4.4.0 from Drupal 4.3.2. I do not know anything about MySQL, or PHP which is why I decided to use Drupal. It handles all of this for me. When I am trying to configure blocks, the following error messages are displayed:

user error: Unknown column 'throttle' in 'field list'
query: UPDATE blocks SET region = 0, status = 0, custom = 0, path = '', weight = 0, throttle = 0 WHERE module = 'queue' AND delta = '0' in /home/banshee/public_html/includes/database.mysql.inc on line 97.

user error: Unknown column 'throttle' in 'field list'
query: UPDATE blocks SET region = 0, status = 0, custom = 0, path = '', weight = 0, throttle = 0 WHERE module = 'poll' AND delta = '0' in /home/banshee/public_html/includes/database.mysql.inc on line 97.

user error: Unknown column 'throttle' in 'field list'
query: UPDATE blocks SET region = 0, status = 0, custom = 0, path = '', weight = 0, throttle = 0 WHERE module = 'node' AND delta = '0' in /home/banshee/public_html/includes/database.mysql.inc on line 97.

user error: Unknown column 'throttle' in 'field list'
query: UPDATE blocks SET region = 0, status = 0, custom = 0, path = '', weight = 0, throttle = 0 WHERE module = 'throttle' AND delta = '0' in /home/banshee/public_html/includes/database.mysql.inc on line 97.

user error: Unknown column 'throttle' in 'field list'
query: UPDATE blocks SET region = 0, status = 1, custom = 0, path = '', weight = 0, throttle = 0 WHERE module = 'user' AND delta = '2' in /home/banshee/public_html/includes/database.mysql.inc on line 97.

When making a PHP block (eg an alternative login block), the resulting block is included/executed at the wrong place. It is included even before the HTML declaration.

The same block displayed in the correct location in 4.3, and if I set the block to HTML instead of PHP, it also renders correctly (without actually doing what I wanted it to do ofcourse ;-)).

Drupalites,

I have finally managed to upgrade from 4.3.2 to 4.4.0. I was also receiving the default theme error, which I have overcome thanks to Marvin error in upgrade from 4.3 to 4.4 which detailed the method to correct that issue.

I notice now when I try and administer filters, the following messages appear:

user error: Table 'banshee_drpl1.filters' doesn't exist
query: SELECT * FROM filters ORDER BY weight ASC in /home/banshee/public_html/includes/database.mysql.inc on line 97.