So, I have a theory here. Several, actually.
1) electromagnetic corrosion
Bombardment with electromagnetic particles and photons over time will produce a 'burnt' appearance on most metal surfaces.
2) Reletivistic shifts in hull structure.
Because Minmatar ships typically have the pressure hull closer to the exterior of the ship (Read: not a lot of armor HP), the relativistic shifts in the speed of light cause an effect called 'quantum tunneling' to occur, in which particles pass through the empty space between each other(
http://en.wikipedia.org/wiki/Quantum_tunnelling) causing minute amounts of gas from the pressure hull to escape and, due to the high energy of the particles at relativistic speeds, bond with the exterior of the hull.
3) Large concentrations of Iron atoms in minmatar space.
Due to the concentrations of Iron particles in minmatar space (What gives minmatar space it's reddish color), most alloys produced in the Republic have higher concentrations of iron in them, as a matter of concentration.
4) Less vacuum alloy-blending
the most evenly blended alloys are produced in a vacuum, in space, were a lack of gravity prevents denser metals from 'settling' near the bottom. In Minmatar production, a zero-gee, complete vacuum alloy blending facility would no doubt be prohibitively expensive, thus, minmatar engineers instead use giant electromagnets to agitate iron particles embedded in the center of a block to be blended. As the iron particles are drawn out of the mixture, they blend the alloy. Some iron particles bond with the exterior of the alloy, giving it it's reddish hue.
Thoughts anyone?