Yeah, I got a little trick that will do that, with Automator. Launch Automator and create an an Application workflow. Add the following actions:
"Get Specified Finder Items" -> here's where you specify the folder you want opened.
"Open Finder Items"
Then save the workflow and drag it to Launchpad. You might wanna change the icon too. Works just like a folder.
The two hierarchies are separate, and cannot be kept in sync without third-party intervention. Even then, there would be difficulties. Note that Launchpad folders have capacity limits that actual folders do not have, and folders within /Applications can contain nested folders, while Launchpad folders cannot.
It's just a coincidence that the apps in /Applications/Utilities match up with the Utilities folder in Launchpad. On my machine, I moved Terminal out of the Utilities folder in Launchpad, but it's still /Applications/Utilities/Terminal.app
Best Answer
I had the same problem. Until now resetting the Launchpad database worked for me. Try:
Note that this operation will reset the organisation of your Launchpad back to default.