All those problems should have been ironed out by now with the latest 2.58 version of AmiUpdate.
Of course the problem is it won't work if you try making an older, faulty version (like the ancient one on the installation CD from OS4.1FE) self-update to the newest, so the way around the Chicken and Egg situation is to get AmiUpdate 2.58 from amiupdate.net and install it yourself, before you try using it to install other things.
At least that's the way I have experienced it, and I know of several others that have e.g. created a new partition, installed FE from the CD, Installed AmiUpdate 2.58, then let the new AmiUpdate install Updates 1, 2, and 3, without any issues.
Best regards,
Niels
