Hi Mike,
It doesn't sound like you're doing anything fundamentally wrong, and I do have a few words of advice.
The too long didn't read version: Don't worry about it. If you want to understand, I'll take the time to explain it, so read on.
First, it is generally preferred to let MC do the mode switching instead of MadVR. MadVR can have problems resetting the resolution and refresh rate after playback is done, and MC does not. As long as you have the modes and timings configured on your video card correctly, you will get the same playback results in MadVR regardless of who does the mode switching. Actual cases where it's essential to let MadVR change modes are rare and can usually be worked around with custom profiles. Why bother with that? Because as I said, letting MC change modes is more reliable. This is not related to your complaint, but it's good advice.
Second, I'm not convinced you actually have a problem. I understand that calculation you're looking at offends your aesthetic sense, but it may not be a real issue. Here's why. That calculation is a prediction based on comparing the video card clock with the audio clock (they never run at perfectly the same rate) and measuring them with the system clock (which also has variance). One thing you may notice is that as you watch the movie, that interval may start to grow. It may start out saying every 4.7 minutes, but after a while it may be 7 minutes, then 11, then 41, then 2hrs, etc. It will change, because it's just a prediction. If it were saying every few seconds, that would be a real problem. While all that is going on, if you have VideoClock enabled, it is making small adjustments to the clocks in the background to make sure things stay in sync, and this also affects MadVR's prediction. (VideoClock is good, so turn it on if it's not already.)
Let's set aside the issue as to whether you would actually SEE 1 dropped frame out of every 6768 frames.
There's a difference between MadVR predicting frames might be dropped, and MadVR actually dropping frames.
What you really need to look at to see if you have a problem are the lines towards the bottom of the OSD, where it reports actual Dropped Frames and Repeated Frames. There are always drops & repeats when playback is first started, and when you fast forward or rewind. Ignore those. Once playback been going for a few seconds, those counters will probably stop increasing. Hit a Ctrl-R to reset those statistics, and you'll see they both go to zero.
Now WATCH your movie. Watch it for those 4.7 minutes, or longer. What you're interested in is if that line towards the bottom showing actual Dropped Frames (it does not display the word actual, but that's what it is) increases.
If you get to 4.7 minutes, and you do not see that Dropped Frame counter increase from 0 to 1, then MadVR's prediction was wrong, pure and simple. And by that time, the prediction is probably not 4.7 minutes any more. Keep watching. If that Dropped Frames counter is not increasing, MadVR is not dropping frames. Period.
So if you watch for a while, and you see actual Drops or Repeats after you've reset the counters, then yes there's an issue. Come back with screenshots of your OSD and other config screens, and we'll take a look.
If you see your Dropped Frames counter stays at zero after the reset, then you've learned your lesson, and come back and tell us all is well.