There are some situations where turning on CaptureFile does not save all the information you see during your session. Here are some pointers for making sure all the information gets saved:
Session Menu
"Save Lines Off Top" controls the saving of text to the capture file when "Capture from Port" is selected in Preferences. Be sure that this command is checked in order to capture the text.
Preferences
Data capture control is only enabled when "Capture from Port" is selected in the Preferences Communications window (in the Edit menu). The command "Save Lines Off Top" has no effect on capture if "Capture from Screen" is selected in the Preferences menu. Note that "Save Lines Off Top" will always control what goes to the Log or Scrollback window.
"Capture from Screen" is the default in CW 1.0. "Capture from Port" is the default in CW 2.0.
TIP: To pause a capture rather than turning the mode on and off, hold down the option key while selecting the Session menu. The Stop capture menu item will say Pause Capture instead. To resume capturing, hold down the option key and select Resume Capture from the Session menu.