NTM -
I see my Benchmade Buddy is still searching for the answer to his "corrosion" (I mean "staining") problem.
If it were me, I would send it back to Benchmade for new clear blade if I were not happy and if Benchmade will swap out the blade. Then I'd hit it with some Breakfree CLP and keep it wrapped in a silicon impregnated cloth to avoid any corrosive staining.
Here is some info from a welding manual about corrosion (rusting) of D2 steels that might be of assistance.
"Extremely high carbon die steel. The steel here is D2. D2 is an old steel, originally used for dies to press and stamp and cut out other metals, and is also used in ball bearings as the load surface. It can be made to be one of the hardest, toughest, most wear resistant tool steel blades, period. It has so much carbon and enough chromium that in the crystalline structure of the steel, in addition to iron carbides forming, forms additional chromium carbides, creating a structure of extremely hard particles, leading to very high wear resistance. This wear resistance is so hard that the knife cannot usually be field sharpened, which may be a drawback. The steel is also not a true stainless, only stain resistant as it usually has only 12% chromium. So blood, tissue, acidic fluids will corrode and stain this metal. The crystalline structure is also apparent in a high polish, and the surface displays an "orange peel" type of pattern, which some consider attractive. It is also expensive."
Here is a link to steel info for knife makers. It is techy but has some good info and interesting comparisions.
http://www.ajh-knives.com/metals.html
If you like very high polished knives the best I have ever seen with mirror like finishes are those of ATS34/154CM (same steel
different name). Here is a nice example of a highly polished blade. Price is a bit steep though!
http://www.rehobothcustomknives.com/KBLV000C.htm
Or here is one knife that you will positively love, IMHO. It will never ever ever rust, corrode, or stain.
http://spyderco.com/catalog/details.php?product=128
Discoloration on a D2, or A2 steel blade wouldn't bother me at all since this steel is not expected to be "stainless".
Good luck! Have a great day!