category/post navigation – not working properly after upgrade

Prior to updating to 3.2 everything was fine, and worked as it should.

After installing the navigation seems to have gone awry.

Pages are fine
2 categories with no subs are ok
All urls from the search engine work and go to their respective pages on the site

Category 1 works ok
Category 2 works ok

Category 3 has 17 posts

clicking on category 3 sidebar nav – returns one post only – post A

clicking on post A in the nav menu returns a 404

clicking on posts B to M (12 separate posts) returns a 404

clicking on posts O,P,Q returns the correct post

Entering a new post with a new category shows in the menu but returns a 404

Theme is Socrates 2.0+

Have tried changing to different themes but it makes no difference.

All installed plug-ins are deleted

Permalinks is set to Custom /%postname%/

I have changed this to /%category%/ /%postname%/ – but it makes no difference

I have tried deleting the posts and categories completely and setting them up again with the same titles, this also makes no difference.

I have now reached the limit of my expertise, and don’t know what to do next.

Its looking at the moment like I will have to delete everything and just use pages for navigation, which in the long run may not be viable.

Fortunately this site has been just sitting on my server for a couple of months doing nothing as I have not had time to work on it and it is not monetized, so I am not that worried if I have to trash it.

Any help or ideas on what else I can try to fix this much appreciated.
Thanks Guys