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Please note - only bit if you are magneto specialist and if you have dealt with this issue before.
Here is the issue that needs to be resolved.
1. I am unable to view newly created categories. Please note - this is an existing site and the old categories are accessible and editable.
2. I am also geting time out error when I try to reindex url rewrites via magneto web interface. This might be related so probably would be the place to start. Pleas note: I was able to reindex url rewrites using command line with no errors. this did not fix the category issue.
Let me know if you need any more details or clarifications.