It seems that the workbench has two file selection modes in the list of changed files - the check boxes, and the actual list-box selection. It also seems that some operations operate on the check boxes (e.g. commit), while others operate on the list box selection (e.g. revert). To add to the confusion, when performing a list-box-selection operation, the list of files that appear in the confirmation dialog is actually the list of files that are checked, not the list of files that are selected!
Issue #2192 wontfix