Found out what happened!
I accidentally forgot to remove writing APEv2 to the tags after helping a member on the forum with something which is a quite a while ago.
Screenshot of my settings if anyone come across the same problem. This was the last thing I thought of.
iTunes does write to the tags.
Steps to resolve same issue.
Drag mp3s to mp3tag.
Use settings in screenshot above.
Remove tags. CTRL+R
Save. CTRL+S
Tags reappear as in iTunes