To understand your issue better, does Dark Souls start up when the controller isn't plugged in? Some basic troubleshooting either way, which I'm sure you've done, but everybody misses something now and then.
Make sure you are using the
latest version of dsfix because old versions
do not work with the current version of Dark Souls.
When installing DSfix, make sure you run the game and turn off AA
before installing.
You didn't mention that you are, but if you are using dsmfix (for any of the other perks it offers) then make sure you use the
unofficial update.
Games For Windows Live (GFWL) gave me a
shit ton of problems when I first installed Dark Souls. Try uninstalling it from your computer, then re-installing it
manually from the
official site, instead of installing it from the DS installer.