Hmm... that's strange. Not sure if this will work, but... Run the "Setup.exe" (Not Graphic Modes setup), and have the resolution be at 800x600. Then, edit your dosboxblood.conf (I believe it's called) file to change the following values:

[sdl]
fullscreen=true
fulldouble=true
fullresolution=1920x1080 (your res)
windowresolution=original
output=openglnb (Depends on the system; openglnb works well for me)

[dosbox]
language=
machine=svga_s3
captures=capture
memsize=64

[render]
frameskip=0
aspect=true
scaler=none

Not related to the issue, but I like to make these changes anyway:

[cpu]
core=auto
cputype=auto
cycles=auto
cycleup=10
cycledown=20

[mixer]
nosound=false
rate=44100
blocksize=1024
prebuffer=50

Not sure if it'll fix it, but these are the settings I use to run and play the game just fine.