OK, I'm guessing you backed up and later diffed the amule.conf on the client account. However, I would not have expected that to change.
All of the remote clients (amuleweb, amulecmd, amulegui) use ~/.aMule/
remote.conf for their configuration information. The command I had you run built the remote.conf file by copying the appropriate settings from the specified file (in this case, a copy of your server's amule.conf).
The existence of the remote.conf, and the password stored there, is the reason that amulecmd no longer needs you to type in the password when you run it. If you temporarily rename remote.conf you will find that amulecmd goes back to its previous behavior.
So, the problem seems to be that when amulecmd asks for the password interactively, it doesn't hash it properly. On the other hand, when it gets the hash from the remote.conf (which in turn got it from amule.conf), then everything works.
Things to try: rename remote.conf to remote.conf.saved and instead use amulecmd with its command-line options to specify all necessary parameters, including password. Does that work? Use amulecmd with the command-line options plus "-w" to create a new remote.conf. How does the new remote.conf compare to remote.conf.saved?
When you have the answers to those, you can of course rename remote.conf.saved back to remote.conf.

EDITED to add a thought: could this be a problem with either unicode or locale? If a user enters a password at two different computers, but the encoding is different between them, will the hashes match?