Custom key config issues with GR and HH

[Railgun]

Hopefully there're others who can help me out here on this, I've been attempting to set my own control configuration for all three games via each's config file and seem to have hit a brick wall:
GundeadliGne has no problems at all with my changes, but with the other two my controls and the default seem to be clashing. I've set movement to WASD, but in GR "S" (down) has me move down whilst rapid firing and "D" (right) has me move right whilst firing off my special/mana beam. It gets even worse in HH, "A" (left) has the game pause every time I press it.

Is there anyway to stop this from happening, a setting (other than changing keyboard mode from 0 to 2 that is, did that) I may have missed perhaps?

Thanks in advance.

Edit:
Running Windows 7 64bit on an AMD Fusion E-350 laptop if it's of an consequence.