UPDATE 24/07/2013: this bug has been fixed. See here.
This post is a rapid update about the bug in QGIS dev that affects the Semi-Automatic Classification Plugin v.2.0.0, which is related to the supervised classification module of SEXTANTE (saga:supervisedclassification).
The SEXTANTE plugin in QGIS dev (for Windows) has switched to the new SAGA 2.1.0 (http://lists.osgeo.org/pipermail/qgis-developer/2013-July/027097.html); the new SAGA module for the supervised classification has changed, and now it requires some new inputs from the command line. In particular, it appears that the supervised classification module requires always an input table (which should be optional) containing the statistics of ROIs, even when the statistics should be calculated by the module, using the ROI shapefile as input.
The SEXTANTE developer is working to adapt his plugin to this strange input requirement, and I hope he will find soon a solution. In the meanwhile, if you run a supervised classification from the SEXTANTE plugin it produces an error; that error precludes the Semi-Automatic Classification Plugin v.2.0.0 from classifying images.
Therefore, if you need the Semi-Automatic Classification Plugin do not update to any QGIS dev version higher than 1.9.0-327; alternatively, use the Semi-Automatic Classification Plugin v.1.8.0 for QGIS 1.8, which has exactly the same abilities of the version 2.0.0.
I will keep you posted.