Please note that I seem to have found a bug in the grid calculus tool.
I used both SAGA GUI (form OSGEO4W) and saga:rastercalculator tool in QGIS console on Windows 7/8.1.
You can find details and actual input and output files here: http://hub.qgis.org/issues/12573
Anonymous
This is not a bug but a feature. If using grids with different grid systems, values are interpolated automatically with a spline function to meet the target grid system.
For convenience I just added an option that allows you to choose another interpolation type. Now you can choose 'nearest neighbour', if you want to reproduce the exact grass map calculator results. Alternatively resample your grids to one single grid system without interpolation (i.e. nearest neighbour) and use these with SAGA's grid calculator. Thank you for pointing at this inflexibility.