I also have the same problem, but it’s mostly because my site is secure. The WordPress says it’s trying to copy a full path of a file, but the full path of the file is not correct for FTP because the user’s FTP account is chrooted to their home directory.
so:
/usr/home/joe/html/wp-content/uploads/
is actually:
/html/wp-content/uploads/
I need to tell WordPress how to get around that with the automatic installer, or there should be some toggle for sites that are chrooted, because at this point, I have to upgrade everything by hand, and that’s a pain. I’d like to be able to have the user do it themselves through the automatic update.
this happens on core updates, as well as plugin updates.