My guess is that when you're traversing a network or NAP that is
dropping 10-20% of its packets, smaller packets would have a higher
survival rate and thus result in better overall throughput due to
the lack of timer based retries.
It probably has nothing to do with MTUs or fragmentation across
the net. Its probably due to the lossy nature of our current
environment (i.e. overloaded NAPs).
A simple test should show this. Slap a protocol analyzer on the line
and see how many retransmitted packets and/or response delays there
are for various MTUs. For heaven's sake, don't change system software
until we know what the *real* cause is! We've got enought kludges out
there already 
Gary Flynn
Network Analyst
James Madison University