james,
the file you refer to is correct, ie it has the correct port
uncommented. (ttyS1).....
the cat commands were very helpful, the output seems to indicate there
is a problem communicating during hot-sync ( the actual program used is
irSync on the Palm, and the linux box uses pilot-xfer ).
using an application called IR Ping on the palm, i was able to verify
that the irattach,irmanager, and irtty are working:

cat /proc/net/irda/discovery 
IrLMP: Discovery log:

  name: PalmE, hint: PDA/Palmtop , saddr: 0x598568a0, daddr: 0x1543ad2b

cat /proc/net/irda/irda_device
irda0,  binding: irda0 <-> ttyS1
        UP RUNNING SIR PIO 
        bps     maxtt   dsize   winsize addbofs mintt   ldisc
        115200  50      2048    7       0       500     40

however, when i try to do a backup using the pilot-xfer i get nothing in
the discovery log, but irda_device log reports same as with the Ping
program running. 
        i think the problem is baud rate.....the README in the pilot-link
package states:
" The default connection rate is 9600 baud. You are welcome to try
higher
  baud rates (19200, 38400, or 57600) by setting the PILOTRATE
environment
  variable, but various machines have various limitations. (Be careful
about
  38400 on a Linux box if you've been using setserial to change the
  multiplier.)"
and the irda_device log still shows bps 115200.
i know from the windows app that the irsync is pretty unreliable for
some reason at speeds above 9600, and i set it to 9600 under windows,
how do i setserial for 9600? or does the serial port automatically set
baud to whatever speed the app (pilot-xfer in this case) requests?
i am pretty sure the Palm auto-baud to whatever rate is sent to it, on
hard wired serial connections, i believe the max rate is 57600.

as far as the commands i used to start irda:
i don't do anything with setserial, boot is currently reporting exactly
same port as in windows, ie com2(ttyS1),irq3
i type:
insmod irda
insmod irtty
irattach /dev/ttyS1
irmanager -d 1 -s 1

then i just start the pilot-xfer:
pilot-xfer -p /dev/ttyS1 -b /usr/local/backup
which then asks me to push hot-sync button on palm, at which point i
start the irSync program on the PalmIII.

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