The color issues seem to be related to a few issues:
The big issue is darkness of print. It would seem that Lego is afraid of printing its black elements too darkly, for fear that the 'outline' and such surrounding the elements would become impossible to see if they printed black any darker. Hence, because black is printed as dark gray, there's less 'room' in the spectrum to print dark gray and regular gray, forcing all the gray shades (white and black included) closer together.
Occasionally, some black elements are printed as nearly black with *white* or light gray outlines, which (IMHO) solves the problem. However, when I asked Lego about doing this with ALL black elements, they said that this has a tendency to make the images too confusing for kids (I was surprised by that, but that's what they said).
Another issue is shading. Essentially when you shade each face of a Lego element a different color depending on the light source, it can make a white piece look partially gray, or a gray piece look partially dark gray, etc. A couple years back, I advocated to Lego that they do away with much of the shading on elements to make the colors clearer, and found out that there's been some internal debate on the issue, which apparently came under discussion again.
According to one source, Lego set designers for a period of time were asked not to use both dark gray and black elements within a single set, to avoid the confusion. That mandate obviously wasn't strictly enforced across the whole lineup, and possibly was removed all together (I heard it back around 2004 or 2005, I think). But obviously Lego is well aware of the problem.
I (and a few other AFOLs I discussed it with) started noticing this probably around the time of the color change. It's possible that the printed colors were altered around that time, although I'm not aware of any comparisons done between black elements in instruction books as printed in older versus newer prints. Certainly that would be enlightening. It could also be that it went unnoticed until Lego started using larger amounts of dark gray, which was a trend that seemed to start around 1999 or so.
One of the interesting notes on this is that a few of Lego's instructions in 1984 (I haven't seen any other years) feature a "color key" showing that "dark gray = black". The instructions for 6030 Catapult, 6022 Horse Cart, and 6061 Siege Tower each feature this oddity. It is especially interesting in 6061-- in 6061, the black elements used in the small castle is printed in "true black" (with white outlines), while the black elements in the siege tower itself are printed in a more dark grayish color. I suppose 6030's instructions are similarly strange, considering that the technic axle within the catapult is done in "true black", surrounded by "dark gray" black. Very odd. It seems each of these sets feature some elements printed in true black (minifig parts, etc), with the "primarily black" models' pieces in dark gray.
[unable to shut up]
It seems that some sets (1888 Black Knight's Guardshack from 1992 being one that I found) actually feature some ELEMENTS that are printed in both "true black" and dark gray. The majority of black elements in 1983, 1984, and 1985 were all printed in "true black", but some time between then and 1992, it seems that Lego veered more to the dark gray standard. Clearly, more research is needed!
... Quick research shows a switch probably between 1987 and 1988, where most black elements through 1987 were printed in "true black", with a few exceptions. Then, somewhere in that ballpark, they started switching some instructions to be printed with a dark gray-ish black, with detailed greebly pieces done in true black, or just with a white outline.