Well, at the moment I am using the current CVS and it is working fine with X-Com apoc. Here is my "dosbox.conf" file:
[sdl]
fullscreen=false
fulldouble=true
fullfixed=false
fullwidth=1024
fullheight=768
output=opengl
hwscale=1.00
autolock=true
sensitivity=100
waitonerror=true
[dosbox]
language=
machine=auto
memsize=64
[render]
frameskip=3
snapdir=snaps
aspect=true
scaler=none
[cpu]
core=normal
cycles=13500
cycleup=500
cycledown=20
[mixer]
nosound=false
rate=22050
blocksize=2048
wavedir=waves
[midi]
mpu401=true
device=default
config=
[sblaster]
sblaster=true
base=220
irq=7
dma=1
sbrate=22050
adlib=true
adlibrate=22050
adlibmode=adlib
cms=false
cmsrate=22050
[gus]
gus=true
rate=22050
base=240
irq1=5
irq2=5
dma1=3
dma2=3
ultradir=C:\ULTRASND
[speaker]
pcspeaker=true
pcrate=22050
tandy=true
tandyrate=22050
disney=true
[bios]
[dos]
xms=true
ems=false
[modem]
modem=true
comport=2
listenport=23
[autoexec]
mount c c:\oldgames
mount d f:\ -t cdrom
c: