Some update about the TexturePacker ATF integration.
It seems that there are currently problems with ETC1 compression on several devices.
Since the files open fine in ATFViewer and on most devices, I assume that it is a problem with Flash on the specific targets.
The problem is described here:
I've now changed the default back to raw compressed - that is ETC1/PVRTC/DXT with LZMA compression - but not compressed with JXR lossless.
You can turn on the compression feature in the GUI or command line (--compress-atf).
I hope that the format now works as it should.