I've tried all those things to no avail. I even compared every setting between my two Macs and couldn't find anything
Then it occured to me that those two machines are actually fundamentally different when it comes to the general setup; my MacBook Pro laptop has a single drive with everything on it whereas my Mac Pro has several physical drives -Mac OSX and all the apps are on a different drive than my home folders After all, I could launch my apps with Alfred, but couldn't get it to locate my files or folders.
I thought I had everything covered in Alfred's Features - Default results - Search scope section where "Include folders in home" was enabled, but obviously it doesn't work in this situation.
So I tried to drag and drop the whole drive volume icon into the "Search scope" section and all of a sudden I could find my files and folders!
It would make sense to have just the path of my own user folder there, but that didn't work. Neither did having the entire /Users/ folder, strangely enough, so for some reason I need to have the entire drive (with the /Users/xxxxx folders on.
So problem solved, but why doesn't "Include folders in home" work, and why do I have to add the entire drive in the search scope?