I too am seeing the same symptoms on my DVI external monitor.  It seems
to only happen when the computer is being used or any program is
hanging.  I would be willing to provide any further diagnostic
information/steps.

OS: 9.04 release x32 Native install
Hardware: T60p

I have two external monitors only the DVI blinks

Screen config:

NEC 2070NX 20"
Resolution: 1600x1200
Refresh: 60Hz
Rotation: Normal
Connection: DVI

Soyo Topaz S 24"
Resolution: 1920x1200
Refresh: 60 Hz
Rotation: Normal
Connection: VGA

Screens are side by side in a "big desktop" fashion:

xorg.conf:

Section "Monitor"
        Identifier      "Configured Monitor"
EndSection

Section "Screen"
        Identifier      "Default Screen"
        Monitor         "Configured Monitor"
        Device          "Configured Video Device"
        SubSection "Display"
                Virtual 3520 1200
        EndSubSection
EndSection

Section "Device"
        Identifier      "Configured Video Device"
EndSection

Section "ServerFlags"
        Option  "DontZap"       "False"
EndSection

Video card from lspci:
ATI Technologies Inc M56GL [Mobility FireGL V5250

Driver:
Default driver (open source I think)

Lsmod:
Module                  Size  Used by
aes_i586               15744  0 
aes_generic            35880  1 aes_i586
nls_iso8859_1          12032  1 
nls_cp437              13696  1 
vfat                   18816  1 
fat                    58272  1 vfat
binfmt_misc            16776  1 
tun                    18820  0 
radeon                342816  2 
drm                    96296  3 radeon
bridge                 56340  0 
stp                    10500  1 bridge
bnep                   20224  2 
vmnet                  47812  14 
vmblock                21028  3 
vmci                   58452  0 
vmmon                  76912  6 
input_polldev          11912  0 
lp                     17156  0 
arc4                    9856  2 
ecb                    10752  2 
snd_hda_intel         435636  4 
snd_pcm_oss            46336  0 
snd_mixer_oss          22656  1 snd_pcm_oss
snd_pcm                82948  3 snd_hda_intel,snd_pcm_oss
snd_seq_dummy          10756  0 
snd_seq_oss            37760  0 
snd_seq_midi           14336  0 
snd_rawmidi            29696  1 snd_seq_midi
iwl3945                97912  0 
snd_seq_midi_event     15104  2 snd_seq_oss,snd_seq_midi
pcmcia                 44748  0 
snd_seq                56880  6 
snd_seq_dummy,snd_seq_oss,snd_seq_midi,snd_seq_midi_event
mac80211              217208  1 iwl3945
iTCO_wdt               19108  0 
snd_timer              29704  2 snd_pcm,snd_seq
snd_seq_device         14988  5 
snd_seq_dummy,snd_seq_oss,snd_seq_midi,snd_rawmidi,snd_seq
joydev                 18368  0 
iTCO_vendor_support    11652  1 iTCO_wdt
thinkpad_acpi          66560  0 
usbhid                 42336  0 
led_class              12036  2 iwl3945,thinkpad_acpi
snd                    62628  16 
snd_hda_intel,snd_pcm_oss,snd_mixer_oss,snd_pcm,snd_seq_oss,snd_rawmidi,snd_seq,snd_timer,snd_seq_device
psmouse                61972  0 
btusb                  19608  2 
video                  25360  0 
intel_agp              34108  0 
agpgart                42696  2 drm,intel_agp
ppdev                  15620  0 
yenta_socket           32396  1 
rsrc_nonstatic         19328  1 yenta_socket
pcmcia_core            43540  3 pcmcia,yenta_socket,rsrc_nonstatic
nvram                  16396  1 thinkpad_acpi
cfg80211               38032  2 iwl3945,mac80211
soundcore              15200  1 snd
snd_page_alloc         16904  2 snd_hda_intel,snd_pcm
serio_raw              13316  0 
nsc_ircc               29328  0 
pcspkr                 10496  0 
output                 11008  1 video
parport_pc             40100  1 
parport                42220  3 lp,ppdev,parport_pc
irda                  197180  1 nsc_ircc
crc_ccitt              10112  1 irda
usb_storage            82880  1 
e1000e                121136  0 
fbcon                  46112  0 
tileblit               10752  1 fbcon
font                   16384  1 fbcon
bitblit                13824  1 fbcon
softcursor              9984  1 bitblit

-- 
Screen blinks randomly on external monitor
https://bugs.launchpad.net/bugs/349943
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