The black Zekroms were from the first run. They're kinda sorta first edition, so to speak. The 'unlimited' run, which is what will be available from now on, are the grey.
Also, it is most definitely NOT a low-ink situation. Having held the two in my hand side by side, they're very obviously different. The most noticeable proof it's not just low ink is the texture - the grey Zekrom's background (not the figure, but the grey part) is rougher than the figure, and much rougher than any part of the black Zekrom cards. This is also on the brighter white Reshiram, and is probably the best way to tell those apart unless you've got really good light. The Pikachu doesn't feel as rough/textured as the Reshi and Zek, but there is also a noticeable difference between them.