This thread a little old, but I had this same issue and thought I'd chime in what went wrong for me.
First, when I did my first ./Configure, I forgot to put the dash '-' before 'Dprefix'. Doing this seemed to mess up the build, since further Configures, makes, and make cleans with the correct flag didn't solve the problem. The issue resolved itself when I deleted the source folder, untarred it again from the tar file, and did the first, fresh ./Configure with the correct command:
./Configure -des -Dprefix=/home/user/localperl
So if anyone is still running into this issue, try deleting the source directory and doing it again with a freshly untarred folder.