What version are you upgrading from? From what I remember, there hasn’t been a database change in a few versions, so it’s probably not even needed (I know it’s still in the FAQ, I’m glad you read it!). You can deactivate and re-activate the plugin to run the database script anyway. Deactivating it won’t delete anything, so you won’t lose any data.
Is there a specific problem you are trying to fix?
I am trying to get this Thumbnail Gallery temploate for NextGen up and running but after following the instructions on the included PDF doc the page is blank. Can you tell me what I am missing? Here’s the page: http://websrvs.com/dev/adam/nextgen/