[popcornmix]

If I set-up 2.0, I have output 2.0 with PCM 6 Channels files and 5 Channels output with DTS/AC3 files (I have 5.0 speakers)
If I set-up 5.0, I have output 5.0 output with all files
AVR displays the right format: DTS, DD or MULTI IN

If changing the speaker layout has an effect then I don't believe you are using passthrough.
Post a debug log after playing a file that should use passthough to see what's happening.