Upgrading Drupal

This is the first time that I have seen this but I tried to upgrade my software from the university computers because my own computer crashed. I downloaded and unpacked Drupal 6.16 and then I moved all my current files into a file called drupal_Old. I then uploaded all the new files to the site. I followed each step in the upgrading sheets verbatim. When I went to run update.php the following scanning software on the universities computer network blocked it and posted that it had blocked it because the software had been tagged and reported as malicious. It now is blocking the entire website. I can access my cpanel and work on the files from behind the scenes, but I still cannot access any of them from my URL.

Hello,

Upgrading resulted in many page not found errors on my site, especially in the admin sections. I've tried clearing caches, running cron and update.php again, etc. Update.php is intermittently accessible, and when it has run it has resulted in unspecified fatal errors. Any advice to help troubleshoot this would be greatly appreciated.

I've upgraded to 6.16 from 6.15. The first time I did the upgrade, my sites/all folder was inaccessible. I've tried 3 more times manually upgrading. Now after updating, I cannot get past the admin front page without getting 404 errors. I see that others here are having similar problems.

My site is close to launching and I'm frustrated. Everything is a mess and I'm thinking of just starting over with another Drupal installation.

I did everything upgrade.txt told me to do. When I run the upgrade script, there's nothing to upgrade according to it, Yet in the reports sections, it tells me in big red letters to upgrade now. The system version is still being reported as 6.15. Furthermore, all my Gallery clean URLs no longer work. I've rebuilt the clean URLs for the gallery plugin, Gallery itself and Drupal and - you guessed it - it doesn't work.

Again, I did everything upgrade.txt told me to do. So what's going on? I don't seriously expect an answer, but surprise me and give me one.

Yesterday i update my drupal site then i get semaphore error when i fix it (i followed forum in here) my modules are dissapear! I cant find and i cant reinstall them, i cant access modules section too ... For this reason i cant open my website again from maintenance mode coz its dissapear too...

Please help i dont want to re install again...

I have update php to:

PHP 5.3.2 (cli) (built: Mar 4 2010 21:52:46)
Copyright (c) 1997-2010 The PHP Group
Zend Engine v2.3.0, Copyright (c) 1998-2010 Zend Technologies

Now on my homepage I am getting this error:

warning: Parameter 1 to profile_load_profile() expected to be a reference, value given in /var/www/html/website/includes/module.inc on line 462.

Please assist.

Jaysunn