I just upgraded my Magento v1.7 to v1.9 without too much complication. All the front end functionality seemed just fine but when I logged into the back end I noticed that two of the main pull down menus were not showing up... "Reports" and "System".
I was about to roll back to my backup until I found that one of my extensions that has it's own top level menu had an option that was a short cut to "SYSTEM -> SYSTEM" so I could view/change some of my system settings.
I don't seem to have any problems adding products, editing any CMS pages or any number of admin type functions. I did find that some items from the "System" menu I could handcraft a URL that would get me there. That tells me it's not an issue with not having the sufficient rights.
Double checked MySQL entries, just poking around and all look OK. I have 3 other admin level accounts and can log in but still no menus.
My issue seems familiar to another Stack Exchange issue from 5 months ago... System, Reports Menu not show in magento 1.9
While someone did offer up a solution the original poster never commented if it worked or not. I tried it and it didn't work for me.
My wild guess is that there is an XML file somewhere that controls what menus show up, what's listed under the menu and what conditions need to be met in order to display the menu. I've been under the hood a fair bit with Magento but real deep in tinkering with CORE config issues.
Any help is greatly appreciated!