I will confess to not being an expert, but as a guy who doesn't know all that much about women's boots, over the knee immediately conjured up an image of shiny, high heeled, and suited for only one profession. It sounds like the ones the OP wore are a totally different type, which may account for some of the confusion on here.
The rule I've suggested for the office when we hire summer interns is that if it would be too revealing to wear around your grandparents, it's too revealing for the office, and along the same lines, if you're wondering if it's too revealing, it probably is and it's better to err on the side of being too conservative.
All that said, I wouldn't worry about what one person is saying if others are complimenting you on your style. If you're close to someone in the office and are at all concerned, maybe say to them, was what I wore yesterday okay, I got some mixed comments. That should be enough to suggest to them that you are really asking and willing to hear both positive and negative comments.