Are you sure this issue is only occurring now that you've updated to v1.8.2?
On my machine this behavior is exhibited by v1.7.8 as well (the behavior being if a target is specified that doesn't exist, it will use the active window, and the command will stop if the active window loses focus or is closed).
EDIT: Did you update from a version earlier than v1.7.8? v1.7.7 and earlier refuse to execute the command when the target is not found, unlike v1.7.8 which executes it regardless.
EDIT#2: If a command contains a keypress action, it is still prevented from executing in v1.8.2 when the "Stop command if target window focus is lost" option is checked.