Saving PDFs in preview flickering screen

So I use preview a lot to take notes in class and have a good number of fairly large (At least I think they are fairly large?) PDF files on my computer. I have been using preview to take lecture notes for about a year now, but about a week ago every time I try to save a PDF on Preview the screen of preview freaks out and starts flickering and just in general acting strange. Has anyone else had this problem? I took it to the genius bar and they reinstalled OS X, and then when that didn't work they did a full factory reset on the computer and it is still happening. Basically their best advice was to use Adobe. However, I have been using preview for years and really have enjoyed using it and I paid too much for this computer to have their basic PDF viewer not work. Any suggestions? I have an early 2015 MacBook Pro 13" with OS 10.12.2 running.