I finally fixed the timeout issue.
It was as “easy” as setting the “Timeout” configuration setting of Apache to a big value (3600 = one hour).
The default is 60 seconds which makes the MOVE operation impossible because it takes much more than that.
After the fix I still get the failure regarding the checksums (but now in the form of a HTTP 400 error).
I will try to debug remote.php and see if I can find out anything.
Then, I will open a new thread so that we can talk about the checksum issue there (this one is a big bloated by now).