Q: FAQ: Transaction Sequence number (Z-Stack, ZigBee) by 656199

ZigBee-2006 TransSeqNumber field passed up in the AF_INCOMING_DATA structure is always 0.

If you look at AF.c in the afBuildMSGIncoming function which created the AF_INCOMING_DATA event to the application, you can see that in version 1.0, the field was populated with the sequence number sent in the message.
In ZigBee-2006 there is no longer an application level sequence number sent. It is up to you to add your own application header information which would contain such a sequence number.