URL Rewrite not working for users created before multi store setup was enabled

[anoopkundal]

We have Magento CE 1.9.1. We recently enabled multi store functionlity to support city wise stores. All the functionlity seems to be setup fine and working as desired. However we noticed one thing is broken. The catalogue view URLs are not working for user accounts that were created before we switched to the Multi Store setup. All the links work fine for not logged in users and for user accounts created after the setup was done. It does not work only for accounts that were created prior to the multi store setup. The users just get redirected to the home page with a 302 redirect to the home page url. The same URL works fine for not logged in users as well as logged in users with the new created accounts.

We have looked through all the customer tables for any mapping. All user accounts are mapped to the original default store ID (which still exists). We have deleted all the Session files, Truncted the core_url_rewrite table and recreated all the indexes again.

Can someone please guide where to look for a solution? 

[anoopkundal]

After an endless night debugging through all session variables and URL rewrites, I firgured out the issue was related to the Custom design -> Page Layout setting in Categories. We use '1 Page layout' for our design, but for some of the categories this was setup to 'No layout updates'. Changing this value got things working. We now just need to work on some navigation issues. So one problem sorted.

Though I still need to understand why was the layout working fine for new users and not logged in users. The problem was appearing for only those accouts that were cretaed prior to the multi store setup. I had cleared all cache, incluidng layouts and also cleared all indexes and created them again. What else is Magento caching and where?