I tried Googling it but to no avail and then today it hit me what the problem might be. I knew that in the past I had to change the codec to QT settings and thought I would try that. That is when I found the issue.

There was recently an update to the Quicktime player on my machine. I did not think anything about it, I just thought it was just another update. Now, I’m not sure if it reinstalled it or I didn’t check the right box but when I went to try to play a .mov in QT it had to re-install itself. After it re-installed the settings for my codec was there and I was able to import .mov’s again into Adobe Media Encoder and Premiere.

So if you are having trouble importing .mov’s into Adobe Media Encoder or Premiere then try updating to the newest version of QuickTime or installing it period.

I hope this helps some of you.