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It sounds like you did a good job weatherstripping the window; it had to have made a difference. I am wondering if maybe she was feeling the draft of the cold air falling off of the cold glass. I would stick with what you are doing and adding the rope caulking may help. I've installed those shrink kits and they really are not that great. They look good for a week and then the tape starts to give way and the plastic tends to fall off in the corners; then you have to try and retape it and it is just a pain. Then if she accidentally pokes it or cuts it during the winter, which is not hard because the plastic is so thin, then it has to be repaired. And lastly, it is a one time use; in the Spring you take them all down and throw them away; waste of money. I would convince her that her money will be better spent by weatherstripping the windows; it will last many years and will perform better. She may want to install some blinds or pull down shades to help with the cold drafts from the glass. In addition if the top sashes are painted or nailed in position, I would seal their perimeters with some caulk; that may help with any air getting around the upper sash.
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Best of Luck, Brian
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Architect
Licensed Architect- 12 years, L.E.E.D. AP, Former Remodeling Contractor- 10 years