RFC3162 notes "As discussed in Section 17.1.1.3, an ACK for a non-2xx
response will also have the same branch ID as the INVITE whose
response it acknowledges."
As a fix, for the INVITE-RESP-ACK scenario, the default has to replaced by an explicit branch-id. In other words,
Via: SIP/2.0/[transport] [local_ip]:[local_port];branch=[branch]
should be replaced in the XML input file to sipp with,
Via: SIP/2.0/[transport] [local_ip]:[local_port];branch=branch=z9hG4bK10_16a832_12341234
There's a start_txn and ack_txn attribute to handle this - see http://sipp.sourceforge.net/doc/reference.html#Create+your+own+XML+scenarios.
(https://github.com/SIPp/sipp is the best place to raise issues now.)