Our final delivery is in 4K flat. Unfortunately we have mixed cameras and sizes. Some true 4K while most is UHD. When I frame flex the linked UHD footage and compare it to the down converted clip in the timeline the AMA looks stretched. Has anyone else had this issue? could it be in the way that we set up the original frame flex?

Did you apply the frame flex to the clip in it's bin *after* editing it into the timeline?  If so try refreshing your sequence (right click > refresh sequence).

Have you set frame flex to something other than stretch? letter box or centre punch. And don't forget to refresh sequence to apply it to pre edited clips.