Make sure you are setting the loop area properly. If you set the punch in and out handles (which are reversed triangles and show a red region between them) that's not going to set the loop area for export properly.
Setting the Loop or Punch start and end points is covered in section 4.1.1.5 in the AmpliTube 5 User Manual.
Hope this helps. If it doesn't work, please contact
IK Support and they'll surely be able to assist you.
This is a short test I did with an upcoming artist preset with the loop start and end points set for proper export (which worked as I was able to export the region you see):