Not sure if it applies here, but I use a utility called "setserial" to
set the "low_latency" flag on the port.

I've heard about this setting and used the following code to adjust it:

        ioctl( ttyfd, TIOCGSERIAL, &ser );
        ser.flags |= ASYNC_LOW_LATENCY;
        ioctl( ttyfd, TIOCSSERIAL, &ser );

Is it right or how can it be setup in a proper way?

I also build my kernel with a
1000hz tick rate. It seems to reduce some of the latency,

How can changing of tick rate affect to the whole system? Ethernet, USB, framebuffer? These subsystems work just fine.

but I have never seen it as high as what you are seeing.

Unfortunately, it's not only me. I talked to one guy yesterday, he uses 2.6.24 kernel and suffers from the same issue.
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