We have a 5406zl as the router for
about 2,500 computers on about
75 2650 switches.
The interfaces on the 5406zl showed
some significant Tx Drops when
I rebooted switches connected to
that port. I assumed this
was because the port was blocked
by STP briefly, but I didn't investigate
further. But you've tried with
STP disabled, so perhaps something
stranger is at work.