Cookies on safari

My school uses Duo security to login to university apps and such. I used to be able to check the "Remember me for 7 days" button but now it won't let me and says that I need to enable cookies. I went to Safari>Preferences>Privacy to make sure that "block all cookies" was unchecked but it still doesn't work. Has anybody been through this and know of a solution. It works when I use chrome but I prefer Safari because of handoff. This problem started when I started deleting files from the computer specifically cache by using the terminal. If this was the problem, what should I do to fix it? Note: This problem is now on all of my iCloud devices, so I turned off safari for iCloud but that didn't resolve anything.