I think this may be the same thing I am seeing.  (I was thrown off by
your words "IPSec tunnel".  You are using gif for tunneling, and
using IPsec in transport mode to protect the gif tunnel.  Perfectly
ok, but not tunnel-mode IPsec, which I erroneously assumed.)

Look at the statistics counters with 'netbsd -s -p ipsec'.  If you see
inbound packets with no SA available, you are probably having the same
problem I am.

I have also noticed occasional problem with packets not matching the
SPD when they should on the transmit side.  So there may be something
subtle wrong with the SPD code that has been tickled by a recent
change.

Has anyone else updated recently and ended up with working
transport-mode IPsec?

-- 
        Greg Troxel <gdt@ir.bbn.com>