You're assuming wrong things. I'm surprised nobody just gave it a try to see by themselves.
Here is how it works, so maybe thing would be stated more precisely :
It's obviously on a 32 bits Version. A 64 bits version just can't launch any 16 bits program anyway as NTVDM has been removed from all 64 bits Windows versions.
There's absolutely no lag at all when using an emulator. It has nothing to do with the program itself, it's only an arbitrary and quite incomprehensible delay when launching it from Windows, or from the shell, or whatever.
You can very easily check by yourslef, launching any Microsoft app provided with Windows itself, such as edit !
By the way, as soon as you launch any DOS program, you also lose your keyboard localization !
Just do this simple test :
Launch the command prompt
type edit -> damn 5 seconds (or so) lag, then the classical DOS text editor opens
type anything -> your keyboard is now in US layout.
About that, adding lh kb16 in autoexec.nt solves the problem, except the AltGr key is disabled so you can't type any "\", "@", etc. You have to se ALT + ASCII code... Note that it worked correctly in Windows Vista (and wasn't needed in XP). From Windows 7, MS provided a faulty keyboard table and never fixed it.
Back to our concern :
It has nothing to do with screen resolution, frequency or whatever, for a very simple reason : full screen mode doesn't exist anymore. You can definitely not launch any DOS program in full screen, period. They always have to be windowed. So obviously, nothing at all changes in the windows desktop display (this too is easy to check before writing !)
However, the idea about Intel based graphics may be a serious hint.
As a matter of fact, it worked a breeze up to LGA 775 motherboards, and the lag first appeared with LGA 1055 chipsets. I could clearly see it (yes, my customers are using programs written in Clipper. Then what ? They do the job perfectly).
So is it connected to integrated video processing in the latest motherboards chipsets and intel processors ?
I can confirm it behaves exactly the same with any processor (from the weakest Celeron to the fastest i7), and that the lag is absent on any motherboard using an LGA 775 chipset or older, whatever the processor and with or without an add-on video card.
At least, these are the facts.
Now about the cure... I'm still investigating. :p
For now, the most satisfying solution I could find is the vDos emulator. Unlike DosBox, it correctly manages file sharing for multi-user applications (though in this case, it's not free). WMWare also works a breeze, though heavier to install (vDos needs almost no installation. It's actually much faster and easier to use than DosBox).
As I said above, launching a DOS program through vDos is immediate : no lag at all. Of course, it's mostly aimed at 64 bits Windows, but it does make using DOS program under 32 bits Windows more convenient, because it removes the damn lag to start with.
On the practical side, our multi users customers actually work through PuTTY connected in ssh to Linux servers running Dosemu. At least, we don't have any keyboard nor display issues in this setup (about display issues, Microsoft has been adding CHCP in Windows, while it made no sense at all, since all DOS progams have always been using the standard 437 code page. As a result, some semi-graphic characters display fancy exotic accented characters instead).
Of course, being able to launch DOS programs under native Windows without the weird lag would be more satisfying. This and the damn keyboard translation bug... It worked allright in Vista, so I'm wondering if the Vista files could be inserted in the latest Windows versions... I still have to identify them.