I'd bet dollars to donut's you have a carriage return character ("\r") at the end of $config{'workingDir'}. Try:

$config{workingDir}=~s/\s+$//g;
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Edit: The carriage return could also be at the front of $filename, but it seems far more likely it is at the end of $config{workingDir}. My guess: the hash %config is probably read in from a file created on a windows system, but the code ir running in *NIX. Windows uses: "\r\n" at the end of a line, *NIX only expects "\n", and hence when reading a line in from the file you are left with an extra "\r" at the end. Another solution would be to run the dos2unix command on the config file to remove the extra "\r" characters.