Upgrading Drupal

since upgrading taxonomy.module released with 4.51 or cvs (same), i cannot add vacab categories or terms:

Fatal error: Call to undefined function: check_query() in /my/path/to/drupal/modules/taxonomy.module on line 784

I was using 4.4 (I think) and recently upgraded to 4.5. I deleted all my files (except MySQL database) before upgrading. Most of the site looks OK. However, in my previous installation, nearly all the modules I installed were working. Unfortunately, with this upgrade, a lot of my modules seem to have gone bonkers including (but not limited to):

I've been searching this forum but I cannot seem to find anyone that has had a similar problem. I upgraded from 4.4.2 to 4.5 and followed the instructions. With a few little tweaks it all seemed to work pretty well, however I use the system for an internal company portal and many of the pages are defined types with the flexinode module. It seems that everywhere we've used that to upload a file, the file link is simply missing now.

I've upgraded from drupal 442 to 4.5 on my localhost server (using WAMP) everything runs ok.

When I uploaded the upgraded instalation and database to the server, it worked ok for a while, (though some strange things were happening with the themes) then crashed, with what I think was the same error message as below.

I completely re-uploaded the instal into a fresh folder on the server and then changed that folder to become my public_html folder, only to consistently received this error message:

I have version 4.1 and want to upgrade to 4.5.
I installed 4.5 and ran the update.php. But it has information only for updating from 4.2, 4.3, 4.4. No mention of 4.1.

I ran the database update script anyway, then got a fatal error message saying that there was no sessions table. So created the sessions table by following the MySQL update info given for 4.2.

I ran the database update script again, and the error message says that I needed users_roles table. So I created that using the 4.4.x upgrade info.

I've upgraded to drupal 4.5 and want to instal the glossary module. Can anyone confirm whether the version I downloaded as glossary 4.5 works with druapl 4.5 or only with the CVS version as it says in the readme.txt file?

I tried installing it and the filter aspect worked properly, but there was no way of directly accessing the glossary, as with 4.4. ?q=glossary offers ALL vocabularies to either view or edit, which I don't want or require...

All advice / clarification appreciated
jbc