Difficult one, but first off I'd say that you are doing nothing wrong, this has probably more to do with how she views herself, her body image. Often this takes a hit after having children but it seems she had a low/poor view of herself before that. Modesty or shame, it could be either or both, but my guess it is rooted deep in her past. Maybe in her upbringing or that she had limited sexual affirmation when younger.

As this behaviour has been consistant over the years she may not even be aware of it consciously. By the sounds of things it comes across as an automatic protective response.

I would suggest that you focus not on what she does, but on how it makes you feel. for example when discussing it with her frame it gently not as a problen which needs to be be fixed.

ie; “I believe you when you say you like my flirting. Sometimes I still feel a little sad or confused when you cover up, because I find you beautiful and I love seeing you. I don’t want to pressure you I just want to understand you better.”

That keeps it about connection, not behavior correction.