From the piece of code you gave us I can't reproduce your problem:
my %config = (workingDir => '/root/working/');
my $filename = 'test.pl';
my $fullpath = $config{'workingDir'}.$filename;
print "Dir: $config{'workingDir'}\n";
print "File: $filename\n";
print "Full path: $fullpath\n";
Produces the output
Dir: /root/working/
File: test.pl
Full path: /root/working/test.pl
Which is exactly what I expected.
So the error is likely in a part of the code that you don't show us, which is unfortunate because it means we can't help you.
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