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While the bottom line is that you need to work the hours your boss wants -- WHY do you think it's an issue now?
It doesn't help that in the boss' mind you come in late -- but since she leaves at 5:10 doesn't SEE you stay until six. She could think you walk out 2 seconds after she does and so you're not staying your entire time. Who know what crazy crap bosses think.
Come in when she wants.
IF you're confident you can work it out, you can try a sit down about it. (if not leave it alone)
You said at first she dropped a hint, then at a later date she showed you a spread sheet with your (in her opinion) work habits and hours and said you were late -- what did you say THEN about it? THAT might have been the time to ask for flex time, point out that staying late allows you finish work the comes in late, position it as good for the company.