I didnt use AVRES but I have done INI files for the ROM I use to make sure the games run in the correct 15K resolution. I have confirmed that it is in fact the case but turning on verbose mode on MAME and checking the used resolution. Mame is definitely using the correct 15k resolution
....some good pictures of the display running, if you can. And it's possible, as with my 6200, that your 6800 is doubling the refresh. What does it say in the OSD in-game on that?
I did some more test. I uninstalled soft15k and re-installed with only the 15k mode enabled. The desktop now appear in interlaced 640x480 and the D9800 OSD report a 15.7khz frequency.
Next I started mame with pacman. The monitor still shows a 31Khz resolution with pacman so it seems that my videocard is definitely doubling the lines.
is there something that need to be tweaked to have a 15k resolution or I need to switch to another card?
Pictures are available here: 
http://cid-e4ecfba58f51d061.skydrive.live.com/browse.aspx/Public?authkey=IDiSaNorwhM%24 here is the verbose output of mame -v pacman:
Parsing mame.ini
Parsing mame.ini
Video: Monitor 00010001 = "\\.\DISPLAY1" (primary)
DirectDraw: Using DirectDraw 7
DirectDraw: Configuring device NVIDIA GeForce 6800 GT
Target refresh = 60.606061
DirectDraw: Selecting video mode...
   640x 480@ 60Hz -> 63.906187
   256x 240@ 60Hz -> 62.276497
   256x 264@ 60Hz -> 62.281695
   288x 240@ 60Hz -> 62.273001
   296x 240@ 60Hz -> 62.272416
   304x 240@ 60Hz -> 62.271903
   321x 240@ 60Hz -> 62.271001
   321x 256@ 60Hz -> 62.271844
   336x 240@ 60Hz -> 62.270362
   352x 256@ 60Hz -> 62.270362
   352x 264@ 60Hz -> 62.270687
   352x 288@ 60Hz -> 70.016089
   368x 240@ 60Hz -> 62.269333
   384x 288@ 60Hz -> 68.475332
   392x 240@ 60Hz -> 62.268760
   401x 256@ 60Hz -> 62.268913
   448x 240@ 60Hz -> 62.267814
   512x 240@ 60Hz -> 62.267119
   512x 288@ 60Hz -> 65.724359
   512x 448@ 60Hz -> 64.491323
   512x 512@ 60Hz -> 64.213469
   632x 264@ 60Hz -> 62.266461
   640x 240@ 60Hz -> 62.266302
   640x 288@ 60Hz -> 64.662233
   720x 480@ 60Hz -> 63.715530
   800x 600@ 60Hz -> 63.389011
  1024x 768@ 60Hz -> 63.044791
DirectDraw: Mode selected =  352x 288@ 60Hz
DirectDraw: primary surface created: 352x288x32 (R=00FF0000 G=0000FF00 B=000000FF)
DirectDraw: New blit size = 224x288
DirectDraw: blit surface created: 224x288x32 (R=00FF0000 G=0000FF00 B=000000FF)
DirectSound: Primary buffer: 48000 Hz, 16 bits, 2 channels
RawInput: APIs detected
Input: Adding Mouse #1: \??\HID#Vid_045e&Pid_0713&Col02#7&ccc6a60&0&0001#{378de44c-56ef-11d1-bc8c-00a0c91405dd}
Input: Adding Gun #1: \??\HID#Vid_045e&Pid_0713&Col02#7&ccc6a60&0&0001#{378de44c-56ef-11d1-bc8c-00a0c91405dd}
Input: Adding Kbd #1: \??\HID#Vid_06a3&Pid_8020&MI_00#7&21e641d9&0&0000#{884b96c3-56ef-11d1-bc8c-00a0c91405dd}
DirectInput: Using DirectInput 7