The categories must be identical at all time points.
Aldwaik and Pontius (2012) describe Intensity Analysis while ignoring possible error in the data.
Aldwaik and Pontius (2013) describe Intensity Analysis while considering hypothetical data error that could account for deviations from uniform intensities.
References:
Aldwaik, S. Z. and Pontius Jr, R. G., 2012. Intensity Analysis to Unify Measurements of Size and Stationarity of Land Changes by Interval, Category, and Transition. Landscape and Urban Planning, 106, 103-114.
Aldwaik, S. Z. and R. G. Pontius Jr, 2013 Map errors that could account for deviations from a uniform intensity of land change. International Journal of Geographical Information Science.