I found that ASR9k with IOS XR 4.x exports NetFlow with broken format! The fieldset length is set to be the length of the whole packet and not length of the template! This makes the NetFlow module to skip flowsets (as it doesn't know when and where they start, as they may have padding)
I have implemented a test code that could detect this and report it in a warning and if it happens it tries to recover the correct length! However, that is wrong! If you have flowset 0 and flowset > 0 in the same packet, there is no easy way to recover correctly the length of the flowset 0 and to detect where the next flowset could start