I tried your code and the returned hash was:
workingDir /root/working/ 
mapFile test.map 
inputFile test.in

[download]
which looks fine to me. One possibility is that you night have a "\r" in the data (did the config file come from Windows?) or in a print statement instead of a "\n".

Update: It is possible to reproduce yur problem with a "\r" appended to the WORKING_DIR in your config file.

In reply to Re^3: problem path stored in hash by cdarke
in thread problem path stored in hash by awsiv

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