This has been a perennial problem since the early versions and it still isn't fixed. This problem appears in NTSC frame rates. I have a recent version of MEP on a Windows 10 machine with fairly high end hardware. There are several aspects to it.
1. Exporting a single frame is not exact. Sometimes the frame you see is not exported. A neighboring frame is often exported. Apparently the export recalculates the frame number, but it should be passed the frame number. Importing a single replacement frame has been a problem in the past, and might still be a problem. It used to overlay the wrong frame, which was obvious only on playback, but looked OK when viewed statically in MEP.
2. This same problem happens when exporting a selected range to a video. Sometimes it starts exporting with the frame before the one you can see, and the last frame is sometimes the one you see at the end of the range, or a neighboring frame.
3. For long video exports, the exported frames do not always line up with the original. The frame rate is also sometimes changed, but not always. The solution is to accurately figure out the original video frame rate using another program such as VLC, then use VirtualDub to copy the export and change the rate back to the original. MEP rounds off the quoted frame rate, so you can not tell what it actually might be.
4. This happens with uncompressed exports, but also with exports to formats such as the lossless Lagarith compression. When doing a Lagarith compression MEP claims that the frame rate is incorrect and quotes the 2 frame rates as the same number???? Then when going to the advanced options, things are changed gratuitously. So when back at the export window the aspect ratio has been altered, but that was not an item changed on the advanced menu.
5. This problem has been happening with NTSC frame rates 23.976. MEP sometimes truncates or rounds it to another value when exporting. This is actually a standard value for movies on Blu-Ray, so it should not be changed.
6. A modest proposal would be to have an option where imported videos are assumed to line up perfectly irrespective of the import frame rate.
7. Also all export menus should be checked to make sure that existing options are not gratuitously changed when going to other submenus. My pet peeve here is that I select 3D Side-by-side export and then go to a submenu and upon return find that the 3D option has been changed. .For some export formats the menus remain the same from one activation to the other, but for other export menus they are changed. So if I select 3D SBS jpg export, when I try to export another frame, the menu has reverted to 2D. But some video exports maintain the selection.
I realize I am in a minority in using some rare formats such as Lagarith or 3D. Lagarith is needed to prevent any degradation in video quality with various generations of editing. Absolute consistency in handling options is necessary no matter how obscure the option.