I am having the same problem too. Since upgrading all links to posts give 404 errors.
I have tried editing and republishing posts, as well as manually changing permalink addresses, but the problem persists.
I too am unclear about what you mean by ‘updating’ the permalinks. I also tried changing the format of permalinks to see if that would update them correctly, but with no luck. Help!!
Changing the permalinks to the default setting appears to have fixed the problem but this is not an ideal solution as setting the permalinks to my preferred format – day and name: /%year%/%monthnum%/%day%/%postname%/ recreates the problem.
If anyone can help this newbie figure this one out, I’ll be forever grateful!
If it of any help. I checked error_log file in the root directory. It has a record repeated many times:
[22-Dec-2008 15:18:51] PHP Warning: PHP Startup: Unable to load dynamic library ‘/usr/local/lib/php/extensions/no-debug-non-zts-20060613/pdo.so’ – /usr/local/lib/php/extensions/no-debug-non-zts-20060613/pdo.so: cannot open shared object file: No such file or directory in Unknown on line 0
Unfortunately I know nothing about Linux and servers to go any further with troubleshooting.