I would like to help you use and understand FET. You can ask the author, the forum or the mailing list anything about using the program or understanding the algorithm behind FET. If you have problems with your datafile, I would be happy to help.
Some words about the algorithm: FET uses a heuristical algorithm, placing the activities in turn, starting with the most difficult ones. If it cannot find a solution it points you to the potential impossible activities, so you can correct errors. The algorithm swaps activities recursively if that is possible in order to make space for a new activity, or, in extreme cases, backtracks and switches order of evaluation. The important code is in the files src/engine/generate.cpp and src/engine/generate_pre.cpp (get FET sources version). Probably, the algorithm mimics the operation of a human timetabler.