To diagnose:

  Install pkgsrc/grahics/xplot.
  tcpdump -w foo tcp
  [do transfer]
  tcpdump -tt -S -r foo | tcpdump2xplot
  [read the README in the xplot sources]
  xplot *.xplot, and look at the plots.

You might also take tcpdumps on both ends, process them, and then

  xplot -x -y -tile linux-capture.xplot netbsd-capture.xplot

for the same connection.  In all of this, you should be able to see if
acks happen when they should, and see retransmissions.

Note that changing kernels changing results doesn't rule out PHY-layer
problems, if the PHY is set up wrong in one case.

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