Hi
I had a similar screen flickering as you describe with DosBox. It started sometimes when the programs switched the screen resolution. It always disappeared as soon as I exited DosBox and returned to Windows.
Sometimes flickering started, and sometime not, unpredictable.
Since I have reduced the screen frequency in windows (now 60Hz at 1152x864 resolution), it disappeared competely. I assume it was a problem of my Eizo F57 monitor when switching between very different frequencies.
My graphic card: Nvidia 8800GTS.
Finally, I can live with 60Hz since I use Windows only for launching Dosbox
.
Everything else is done by Ubuntu Linux
regards
Juergen