If it does have to do with those data corruptions you've been reporting, then this probably won't help. But just so you've got some field data to work with:
In "Find it!", I'm loading ATF files from a server, so I decided to include only one compression type in a single ATF file, and download just that file. I'm using the following code to decide which format to use:
var fallbackFormat:String = SystemUtil.isIOS ? "pvrtc" : "etc";
var currentProfile:String = Starling.painter.profile;
var profilesNotSupportingEtc2:Array = [
"baselineExtended", "baseline", "baselineConstrained"];
var optimalFormat:String =
profilesNotSupportingEtc2.indexOf(currentProfile) < 0 ? "etc2" : fallbackFormat;
So, I'm preferring ETC2, since that has the best quality, and otherwise I'm falling back to "etc" on Android or "pvrtc" on iOS. With that setup, I haven't seen a single error log concerning ATF files.
To create the ATF file, I'm using these arguments:
png2atf -c [compression_flag] -r -n 0,0 -i [out_image_png] -o [out_image_atf]
Again, I don't know if that really helps – just wanted to tell you about one specific setup that I know works reliably. 😕 Which ATF settings are you using?