The option 'No Frames in Checkout' in Design Options | Miscellaneous used to only strip out the frames from an Actinic framed theme for the checkout area. In version 6.0.2, this option also works for external framesets.
Try creating a new custom property in 'Advanced | Custom Properties' called 'ACT_SETUP_FRAMES_OFF'.
You don't have to supply any values for this - it will just act as a switch to nuke all frames when you enter the checkout. Look at the context-sensitive help (little '?' in the corner) for the 'No Frames in Checkout' field for more details.
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