Whenever it's time for you to upgrade modules on your site, you should have a checklist of the steps involved. One step I've recently added to my checklist is to clear the site cache just prior to uploading the updated module files.
With over 4,000 available modules, there's no way that anyone can know what each and every single module does. In my opinion, many developers often resort to writing custom modules too quickly without doing their due diligence in looking for an existing module to accomplish the same task.
When I'm working on a site that I think might require a custom module, there's a few steps I take before I break open my code editor (currently Espresso).
One thing that consistently trips up both new and experienced developers when enabling a new module are "permissions". I can't tell you how many times I've enabled a new module then cursed my computer for a few minutes thinking that the module wasn't working properly - only to realize that I forgot to set some arcane permission on the admin/user/permissions page.
So, next time you download and enable that shiny new module, be sure to not only configure it using its settings page, but to check its permissions!