Well i don't know of a fix for the issue u have, but i do have a tip and you might be able to fix the issue you have this way as well. But if you plan on transfering files from one mac to another esp. if one is either an older mac or a portable. you would always want to make one or the other a target disk instead of two stand alone mac's.
Why, because your eMac's older and the data transfer might be failing or can't process the data fast enough to get broken down to bits to be put back on the other end thru the cat5 line.
But to transfer files of over 1 GB i would recommend you start the iBook in target disk mode. But since your eMac is the one with some issues put the eMac as the target.
To connect two mac using TDM (Target Disk Mode) you will need to get either a 6-pin IEEE to 6-pin IEEE firewire 800 cable, a 6-pin IEEE to 9-pin IEEE firewire 800 cable, or a 9-pin IEEE to 9-pin IEEE (if your eMac has a 9-pin port) firewire 800 cable.
Then you connect the cable to one of the eMac's 6 or 9 pin ports and the other end to one of the iBooks firewire 800 ports. (the iBook has both the 6 pin
and the 9 pin.
To start up as the target disk you press and hold T immediately after pressing the power on button. once you see the firewire symbol bounce around the screen you can let go.
Now its like connecting to a external hard drive.