The client produced base64 data with encode_base64() from MIME::Base64 like this:

my $base64 = encode_base64("<some data>");
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This seems perfectly fine. Later these data were sent to the server:

$sock->send("<data>$base64\n") or die "Can't write to $socket";
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This also seems perfectly fine. Now a new parameter was added:

$sock->send("<data>$base64<param>\n") or die "Can't write to $socket";
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The new parameter was ignored by the server when it processed the command and seeing what was wrong was not easy. Finally debugging at the server side showed that the client sent the new argument as a command by itself. This was very strange. Then I thought that maybe a newline somehow came between base64 data and the new argument... Reading the docs revealed that encode_base64() by default returns the data with a newline at the end!

  encode_base64($str, $eol);

    Encode data by calling the encode_base64() function.
    The first argument is the string to encode. The second
    argument is the line-ending sequence to use. It is
    optional and defaults to "\n".
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The fix was easy.