I think we need to address the preverbal elephant in the room:
Why does being salaried imply it is ok to be late (even 5 minutes) or not be as punctual, if not more so, than an hourly employee?
It's like the old saying: Time is money; if you're not making the company money then you're costing the company money.
This is a fundamental principle most managers, executives, and business owners believe in vehemently; furthermore, there is a lot of merit in the belief as many employees (salaried and hourly alike) will often abuse schedules, breaks, lunches, etc. regardless if it costs the company money or not.
Preface / Disclaimer: I'm not sure what your particular labor agreement (contract or otherwise) states or what country you are in and/or your employer originate/operate from, so I will avoid any legal arguments or advice regarding labor laws and such. However, I will note that you seem to be attributing being a salaried employee to having a flex schedule of some sort (at least in start time and end time) when these generally are not equated with one another unless specifically stated in your labor agreement. If it indeed is (or any other pre-agreed condition of employment regarding schedule and/or start/end time exists) then that is a relevant omitted detail which would affect my answer (and likely many others).
I'm going operate on the assumption that there are no relevant details being omitted.
Let's refine what it means to be a salaried employee. There are 3 traits of salaried employees that are often noticed (and frequently expected):
High Availability: Since you may not "punch a clock" everyday, doesn't mean you don't need to be available much more often than an hourly employee. Actually, it's a common experience that salaried employees should be at their desk at least 30 mins to 1 hour before their regular start-time.
Achieve Results: Salaried employees (generally considered to be managers, see point #3) are expected to achieve a result for the company even if they have to put in more hours. Salaried employees need to be available and on-hand (whether that be physically or virtually) to handle problems and achieve results. Salaries generally have overtime built into them for this exact reason. If you perform your essential duties in less than 8 hours per day then that is fine and you may be able to leave early in many cases; however, if a crisis erupts either early in the morning, late at night, or during off-time (e.g. weekends, holidays, vacations, etc.) you're still expected to handle those issues. Managers don't ever "leave" work but rather just scale back their availability and response time to a day or two at the most.
Management / Leadership: Salaried positions are usually reserved for managerial level positions (generally speaking). Even if you're not an actual manager in either title or authority, the prestige of the compensation of the position generally dictates that you hold yourself (will be held) to the same standards as a manager would be.
With these traits in mind, as most senior professionals have, you should be able to see why your manager expects so much of you. Being a salaried employee is akin to being a manager (often just from tradition and prestige of compensation) so being "late" everyday is looked down upon severely by more traditional and senior managers. The only "excuse" is if the position requires frequent travel, but that only works a couple of times until it looks like the person has poor travel planning skills.
When it comes to punctuality, a good rule of thumb is as follows (or often an unspoken rule): being on-time is late, being 30+ minutes early is on-time, and being late is quitting. (Take with a grain of salt)
Theory #1: The Improvement-for-the-sake-of-Improvement Hypothesis
It's not uncommon for organizations and senior management to want to always be improving their company and employees. This could be the same philosophy being propagated down unto middle management whereby they must find something in every employee that could be improved upon.
Theory #2: The Almost Good Enough Hypothesis
It could be, since you say you do very well in your performance reviews, that your manager would like to promote you to a senior or lead position of some sort; however, her manager or senior management frowns upon tardiness and considers that a showstopper for such promotions. You indicate she gives you this feedback in a pseudo off-the-record fashion (it's not formally written down) indicating she might be trying to make it apparent and hint at the fact that this is an important trait to her boss/senior management without putting it to paper (thereby hurting your chances).
Theory #3: The Perception Hypothesis
It might be that your behavior is inappropriate given your labor agreement while others might have agreed upon a later/different start time in exchange for less pay, less/shorter breaks, less lunch break time, etc. While it may seem that they're violating the rules, it could simply be that you're operating on your perception of facts without knowing their specific labor agreements compared to yours. Of course, they may be getting similar feedback as well but don't seem to care or show it as much.
Theory #4: The Everyone's Buddy Hypothesis
This is kind of self-explanatory but when you're good friends with almost everyone ("everybody's buddy") or can garner sympathy from almost everyone, you can get away with a lot. It can also depend on your colleagues' track records / history in the company that they are given slack and latitude regarding when they show-up. Similarly, it's like if you make the company $1 Million in sales annually and you're 15 minutes late everyday, it's perfectly acceptable in many places. It's like having connections and knowing somebody in the company without actually needing to know anyone. Best advice: just ignore it and accept that high-school popularity contests still exist in adulthood and beyond. It's sad but unavoidable.
Theory #5: It's All Relative (The Power Trip Hypothesis)
Sometimes you just can't please your boss no matter what you do and they want to nitpick at you and flex their management muscle because of one unknown reason or another. Only solutions are: ignore it or find a different job/department.
Hope this all helps, best of luck! :)