Why+am+I+missing+certain+nominal+or+string+values+from+sparse+instances?

Internally, Weka stores all attribute values as double precision floating point numbers. In the case of nominal or string attributes these numbers are interpreted as indexes into the set of values for the attribute in question, with 0 corresponding to the first value, 1 the second and so forth. Because sparse data does not explicitly store zeros, any instances containing the first value (with index 0) of a nominal or string attribute does not show this value when printing out an ARFF file that is sparse format.