In your first example the \r is enclosed in back-quotes which interpolate the same as a double quoted string, so \r gets translated to the carriage return character.

In the second example the \r is enclosed in single quotes which do not interpolate so it contains the two characters \ and r.

You need to enclose the string in double quotes: 

my $value = qq[ -c "normal \r" -c wq ~/vimwiki/testing.md];

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In reply to Re: Running command with backslash not working as expected by jwkrahn
in thread Running command with backslash not working as expected by nysus

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