While working through an exercise for the class I teach I noticed that intersect was returning empty output (green file) for an intersect. On inspection of the input files attributes (both BED files, neither including strand information/column) it was clear that the strand column specification was wrong (showed column 1 with box ticked). One bed file had four columns and resetting the strand value by unticking the box worked. The other bed file had only three columns and it was not possible to untick the strand box. Attempting to do so and saving made no difference; the strand box with column 1 specified remained ticked. Re-running the intersect still yielded an empty file. A final attempt to reset the column tick box on the file attribute was to use the auto detect option. This seemed to work and the intersect then yielded a non-empty output file.
It seems to me that this behaviour (automatically setting the column flag for strand to column 1) is an undesirable behaviour, and to have the UI for file attributes resist resetting the flag for strand column is an example of a broken UI.