LAOS Laser

Converting a Morntech lasercutter to laos I'm having an issue with it's endstops.
Things I checked:

• The Xhome and Yhome are individually connected to ground when I press a endstop.
• I measure 1k ohm resistance between the R26 and R27 inputs into the OPTO-IN and the VEndstops when the endstops are pressed, otherwise infinity.
• When I run the test firmware led 1 and 2 go on and off properly when I press the endstops.
• I've tried changing the x.pol and y.pol from 0 to 1 and that didn't matter.
• I'm listening to the MBED with a serial reader on my computer, pressing the endstop doesn't output anything (moving does)
• I'm using the SD card from a already working (smaller) laos lasercutter, and thus tried the working firmware.
• I also downloaded the latest version of the firmware and tried that version

Serial output at startup:
@LAOS v0.3Dec 29 2012 15:52:17...
BOOT...
TEST SD...
SD: READY...
START...

Open config file: 'config.txt'
ConfigFile:ConfigFile (config.txt)

ConfigFile(config.txt)

Local configfile

name: /local/config.txt

'net.ip'='192.168.1.112 '
'net.mask'='255.255.255.0' (default)
'net.gateway'='192.168.1.1 '
'net.dns'='192.168.1.1 '
'net.port'='69 '
net.port: numeric value=69
'net.dhcp'='0 '
net.dhcp: numeric value=0
'sys.autohome'='0 '
sys.autohome: numeric value=0
'sys.autozhome'='' (default)
sys.autozhome default (0)
'sys.nodisplay'='0 '
sys.nodisplay: numeric value=0
'sys.i2cbaud'='0 '
sys.i2cbaud: numeric value=0
'sys.cleandir'='' (default)
sys.cleandir default (1)
'laser.enable'='0 '
laser.enable: numeric value=0
'laser.on'='0 '
laser.on: numeric value=0
'laser.pwm.min'='0 '
laser.pwm.min: numeric value=0
'laser.pwm.max'='90 '
laser.pwm.max: numeric value=90
'laser.pwm.freq'='1000 '
laser.pwm.freq: numeric value=1000
'x.rest'='350000 '
x.rest: numeric value=350000
'y.rest'='200000 '
y.rest: numeric value=200000
'z.rest'='' (default)
z.rest default (0)
'e.rest'='' (default)
e.rest default (0)
'x.homedir'='0 '
x.homedir: numeric value=0
'y.homedir'='1 '
y.homedir: numeric value=1
'z.homedir'='' (default)
z.homedir default (0)
'e.homedir'='' (default)
e.homedir default (0)
'x.invert'='0 '
x.invert: numeric value=0
'y.invert'='0 '
y.invert: numeric value=0
'z.invert'='' (default)
z.invert default (0)
'e.invert'='' (default)
e.invert default (0)
'x.pol'='0 '
x.pol: numeric value=0
'y.pol'='0 '
y.pol: numeric value=0
'z.pol'='' (default)
z.pol default (0)
'e.pol'='' (default)
e.pol default (0)
'x.scale'='-158516 '
x.scale: numeric value=-158516
'y.scale'='158516 '
y.scale: numeric value=158516
'z.scale'='' (default)
z.scale default (200000)
'e.scale'='' (default)
e.scale default (200000)
'x.speed'='1000 '
x.speed: numeric value=1000
'y.speed'='1000 '
y.speed: numeric value=1000
'z.speed'='' (default)
z.speed default (100)
'e.speed'='' (default)
e.speed default (100)
'x.home'='350000 '
x.home: numeric value=350000
'y.home'='200000 '
y.home: numeric value=200000
'z.home'='' (default)
z.home default (100000)
'e.home'='' (default)
e.home default (0)
'x.max'='350000 '
x.max: numeric value=350000
'y.max'='0 '
y.max: numeric value=0
'z.max'='' (default)
z.max default (200000)
'e.max'='' (default)
e.max default (1000000)
'x.min'='0 '
x.min: numeric value=0
'y.min'='200000 '
y.min: numeric value=200000
'z.min'='' (default)
z.min default (0)
'e.min'='' (default)
e.min default (0)
'motion.homespeed'='50 '
motion.homespeed: numeric value=50
'motion.speed'='50 '
motion.speed: numeric value=50
'motion.accel'='500 '
motion.accel: numeric value=500
'motion.enable'='0 '
motion.enable: numeric value=0
'motion.tolerance'='100 '
motion.tolerance: numeric value=100
~ConfigFile()

CONFIG OK...
MOTION...
steps_per_mm_x 158.516006...
steps_per_mm_y 158.516006...
steps_per_mm_z 200.000000...
steps_per_mm_e 200.000000...
accel 500.000000...
Motion: double=8, float=4, block=76
Direction: 8388608
ofs: 0, scale: 921
FIXED IP...
Ethernet Setup...
mbed IP Address is 192.168.1.112
SERVER...
TFTPServer(): port=69
RUN...
Homing skipped: 0
Entering display@

Anyone have any tips on what else I could check?