URL/Path alias not working correctly

Hi,
We've identified a problem on our Drupal sites (4.6.3, Box Grey/phptemplate) where some of the URL/path aliases are not working. Nodes *are* being given aliases when created but the browser is not picking them up.
This doesn't seem to be a problem with Drupal for the following reasons:
- Clean URLs are working;
- URL/Path aliases typed manually into the browser work. The site recognises them.
- URL/Path aliases *are* working on articles published *before* we upgraded from 4.5 to 4.6
- This issue affects *all* types of nodes. There was an issue with book nodes and path aliases but this seems to have been fixed in 2004.
At the time we upgraded we began to use a common codebase where all subdomains are redirected to a common root directory public_html/460 using an apache virtualhost directive (as described here: http://drupal.org/node/20663#comment-36880 ). These are created by our host as we don't have access to the apache config files.
So, I think the issue is to do with the Apache side of things. I've looked at the .htaccess file and there is this section...
-------------------------------------------
# Various rewrite rules.
RewriteEngine on
# Modify the RewriteBase if you are using Drupal in a subdirectory and
# the rewrite rules are not working properly.
#RewriteBase /drupal
.
.
.
# Rewrite current-style URLs of the form 'index.php?q=x'.
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