One way to figure out why ARFF files are failing to load is to give them to the
weka.core.Instances class. In the SimpleCLI or in the terminal, type the following:
java weka.core.Instances filename.arff
where you substitute
filename for the actual name of your file. This should return an error if there is a problem reading the file, or show some statistics if the file is ok. The error message you get should give some indication of what is wrong.
nominal value not declared in header, read Token[X], line Y
If you get this error message than you seem to have declared a nominal attribute in the ARFF header section, but Weka came across a value ("X") in the data (in line Y) for this particular attribute that wasn't listed as possible value.
All nominal values that appear in the data must be declared in the header.