Without insight into the source code, it's nigh impossible to diagnose this.
It could have something to do with how the file dialog returns the path, it could be a windows->Linux(like you said, encoding) issue, it could be a ridiculous number of things without knowing how the program actually works.
I'd like to see the code that retrieves values from the textbox and the file chooser at least, the difference is likely to be there, as by the way you describe it they do the same thing(I'm assuming here the file is always on the server, you're just getting the location in different ways, correct?).
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