Run rules on folder contents misses some files

I made 3 rules to run when I download documents from the "File This" website. When I download files from there, they download in an archive folder. Rule 1 is to unzip the folder. Rule 2 is to run rules on all files inside the folder to file them in my Evernote. Rule 3 then deletes the folder.

The problem is that only one file is filed with Evernote and the rest are ignored.

I suspect if you don't have a separate rule to go into subfolders, then your setup is wrong. Read the sticky article on going into subfolders. If you post the rules in more detail, I can provide more assistance.

The 2nd rule I have is to simply "run rules on folder contents". What could be set up wrong?

Then you combine the logic of two rules into one incorrectly. Read this article: https://www.noodlesoft.com/kb/going-into-subfolders/

If you are still having problems with it, then post the specific rule so I can see where it may be going wrong.

There aren't any sub-folders in the folder I want the rules applied to. The website "File This" stores files like bank statements and bills from my accounts for me. When I download one, I have a Hazel rule for each type to change its name and file it into my Evernote account and then delete the file from the Downloads folder.

When I select more than one file at a time to download, the website downloads them as an archived folder with each selected file inside.

I have three Hazel Rules:

Rule 1 checks the name is "filethisdownload" and is an archive and unarchives.
Rule 2 checks that the folder name is "filethisdownload" and is not an archive - run rules on contents which is supposed to put each one in Evernote where it is supposed to go (this is where only the first one is done)
Rule 3 checks the name is "filethisdownload" and paused for 3 minutes and moves it from Downloads to the trash.

Run rules on folder contents doesn't do anything but have Hazel go into the subfolder. I don't see where you are having Hazel do anything with Evernote. If you are putting it in with the same rule as "Run rules on folder contents", then that is incorrect. Again, see the article as it points out specifically that as something to avoid.

OK, so if I have a folder inside the Downloads folder with one or more PDF's inside, is there a way to have Hazel simply move all of them up one folder so they are all in the Downloads folder? Once there my other rules which watch the Downloads folder will take over and file each one in Evernote.

Yes. You'll need the rule to tell Hazel to go into subfolders. Then you'll need another rule to check if it's subfolder depth is greater than 0 (meaning it's in a subfolder), and move it up (you can set "the enclosing folder" as the destination of a move).