I had this too and resolved it by playing around with the video settings inside the dosboxwc3.conf file, unfortunately I don't remember which setting sorted it out for me, so here's what I have for video settings...
fullscreen=true
fulldouble=false
fullresolution=desktop
windowresolution=desktop
output=ddraw
autolock=true
sensitivity=100
waitonerror=true
priority=higher,normal
mapperfile=mapper.txt
usescancodes=true
edit:
oops ... little bit of a necro-post, my bad, but it might be helpful to someone at some point.
Dolemite007: Hey kids...I just picked up WC3 here on GOG and am re-living some old, fond memories. I had some issues with the video cutscenes running choppy, but it seems that I licked 'em by messing around with the CPU settings in the CONFIG file. However, there's another video issue where when the camera angle changes there's often a split-second graphic glitch effect and I have no idea how to fix it. Any suggestions? Thanks in advance!