Yeah!! solved it. Well actually I haven't solved it but I got it working.
1. Booted up Knoppix.
2. Copy over the firmware.agent file from /etc/hotplug in /KNOPPIX to the /etc/hotplug folder on the Gentoo install (on hda3 in my case, remember to mount the hd with read permissions).
3. Copy over the /usr/lib/hotplug/firmware/isl3890 file in /KNOPPIX to the equivalent folder on the Gentoo install.
In my case it was the firmware.agent that was shagged.
EDIT: dangertools says this might be due to a change in file path. see
http://forums.gentoo.org/viewtopic.php?t=238544