Most likely, the files '.\1', '.\2' and '.\3' do not exist. The copy command
copy archive.rar+1 appends the content of file '1' to the .rar file. If the file does not exist, it is treated as if it were empty. The hash changes nonetheless because without the '/b' flag, the command also appends the character 0x1A. Since all files found with (*.rar) were the same to begin with, adding the same bytes to every one will result in three exact same .rar files with the exact same MD5.
You can make sure the MD5 values are different after running the script by creating the files '.\1', '.\2' etc. with different contents. If you simply want to append the characters, you may want to use something like
echo !Counter! >> %%1 instead. The resulting files will not be valid rar archives anymore, of course. For that, you will need a rar tool with a command line interface.