Pressing F1 will open the help system in many applications. Make sure your command targeting settings are correct.
Command targets can be set at the profile level, using the "Send commands to this target" option on the profile options window, or at the command level, using the "Send command to this target" option on the "Add/Edit a Command" window.
The "Perform a Window Function" action can be used to switch targets on-the-fly, if the "Set command to target this window" option is checked, as can the "Run an Application" action using the "Set command to target launched application" option.