Hi Dexje,
The issue you're seeing is due to the video card not being properly reset on wake-up. When you shut Windows 10 (and 8, 8.1), it actually goes to sleep instead of really turning off as it did in Windows 7. This makes the subsequent boot process faster, but probably drivers are loaded directly on ram from a disk image, bypassing their startup sequence.
CRT Emudriver relies on a hook in its startup sequence to clear some stuff that ATOM-15 turns on during boot in order to output interlaced modes properly. When this is bypassed, you get that issue. If you restart your system manually, Windows goes through the full boot process instead, which leads to proper driver initialization.
A possible fix is to force Windows 10 to always shut the system completely instead of going to sleep. I don't know if this is possible these days, probably it is.
Another fix, even if it's an ugly one, is to force a reset of the video card device on Windows startup. Check this
post.Finally, you may get rid of the issue by avoiding the use of interlaced modes on boot. Since you have a 31 kHz monitor, the interlace mode you must be seeing is 1024x768i for the Windows logo. Try to change the Windows startup options to use "base video" (640x480) instead. This will disable the fancy logo and set a Vista-like one. I don't now if this is even possible on 10, it was on 7.