Linux 3 file system format? I assume you mean Linux ext3?
As for dumping it, you should have a look at some of the
bugs in the early releases of Beyonwiz firmware (the link refers to 2007 vintage software, Beyonwiz PVRs are now pretty solid). I had some similar types of experience with early Topfield 7000 firmware (I was a beta tester for both, but am no longer a Topfield beta tester). Many PVRs get released too early in their software development, presumably in a drive to get to market early. It wouldn't surprise me much if the same was true of the Humax.
Have you tried formatting the external HDD, then shutting down completely (mains power off) and then restarting before trying the copy? The mains power off suggestion is because I have no idea what the various power saving settings do to the Humax's state in its standby mode. I don't own one.
Surely it would be better to ask about problems like this in a dedicated Humax forum, rather than the Humax area on the IceTV forum, since this sort of problem really has nothing to do with IceTV at all.