I'd first remove the APEv2 tags:
- Goto File → Options → Mpeg and enable only APE under remove and press OK
- Select the files and remove the APEv2 tag via File → Remove tag or Ctrl+R
Then, again at File → Options → Mpeg, enable everything under Remove and make sure to disable reading and writing of APE if you don't use that and/or have obvious problems with other apps.