Hi Szymon,
I'm currently facing the exact same error you are describing in your post. One year ago, running NW AS Java 7.02 SP16, the approach you mentioned (fixing the folder structured) worked for me. Today, running NW AS Java 7.31 SP17, the approach does not work anymore. To boot, the zipped config I'm trying to upload is standard (non-touched by me) and its contents are all directly in the archive (no folders involved). I've also extracted the xml and its dtd and ran a validation check via XMLSpy, which succeeded. I've also tried raising the trace level of the UWL application to debug mode, but there is no information thrown which would be more detailed than "unable to read file", i.e. no concrete line or sub-file reported by the parser (which I hoped for).
Any other idea? :-/
Cheers, Lukas