Cloud mask - SNAP sentinel 2

try this.

Raster > Subset

Select yes and run without any change.
Should be done in about one second

Open your your new (virtual) product > File > Export > GeoTiff (not GeoTiff/ BigTiff)
There select “Subset…” and choose your desired band in “band subset”.

Worked for me. Please also see my thoughts on virtual resampling: