I too run a lot of Matrix stuff and apart from the woeful 'Alea Jacta Est', the other 20+ games and CivV etc run fine.
I had same problem as you with this game but maybe keep trying along lines below...
Sequence of my events was:
- install, reboot, start game - problem.
- reboot, start game, game patched from 1.00 to 1.02, reboot- problem
- looked on here - saw reference to antiviral, disabled in system tray, start game - problem
- checked antiviral was disabled and it 'was' however - Norton keeps some things running even when disabled from tray!, opened Norton and disabled all real time protection for five hours...
- reboot and success...at least I can start...
Now onto next issue which I cant see a fix for ... 'Black screen of game' - just about to post
And if you wondering what all the reboot is - I have an ssd so its pretty quick and eliminates any other issues but i suspect its probably not req'd...good luck.