I can confirm DWM is not causing it.
I've suspended winlogon and killed DWM.exe and confirm that it stays closed, yet any output other than ddraw still runs slowly. Furthermore, DOSBOX runs like a dream on the same machine in Windows 7 even with DWM enabled.
I have confirmed that there are no AppCompatFlags set in the registry.
I have discovered that setting frameskip to 1 makes the game run at a perfectly stable rate, but of course choppier.
The problem is...the CPU is an i7 running TIE Fighter at 320x200, so it really shouldn't be necessary.
I'll try messing with drivers to see if that's the cause, but on my i7 Laptop with just the integrated Intel graphics the same thing happens. It's something Windows 8 specific that's causing this.
Are there any log files that could help figure out what's going on? There's nothing in stdout or stderr (blank) that suggests a problem.
Also, to clarify, it's not just general slowness, but like clockwork it gets periodically much slower (slow enough to see each frame being drawn from top to bottom) every second, and then back to "normal" (but still too slow) speed. ddraw and custom builds using direct3d outputs are the only outputs not affected, yet even ddraw is not viable because if the windowed/fullscreen resolution is any higher than 640x480 or so then it gets very slow as well, due to Windows 8's ddraw emulation.
EDIT: Okay, I figured it out! It's caused by Nvidia video drivers forcing vsync. It gets even worse if it's an Adaptive setting. So if anyone else has Windows 8 and a slow DOSBOX, turn that off.