Trunking effect on latency

[Vann H. Walke]

I'm hoping for some help with some network configuration questions:

We're working on a 72 node, 144 processor system connected with gigabit
over copper.  Our current network configuration is essentially a "fat
tree."  

The bottom layer of switches (9, Dell 10-port 5012) each have 8 nodes
attached to them. These switches are attached to 3 mid-level switches
using a 2 port trunk (2Gb trunk).  The mid-level switches are connected
to the top level switch (Dell Powerconnect 24 Port, 5224) using a 4 port
turnk (4Gb).

After doing some performance analysis of our application, we determined
that none of the trunks were being used at anything close to 1Gb.  If in
this situation we were latency limited, my theory was that removing the
mid-level of switches and going without the trunks would improve
performance (by removing the latency added by the additional switches).
However, performance with each of the smaller switches connected
directly to the master switch was considerably worse.

Any ideas on why this is the case?  Can trunking improve latency?  Is
there effect on the network that I'm missing?

Thanks,
Vann