I got Gold's CIA from that iso site and it worked fine. I messed around with the CIA and did everything to get Crystal working(Also I did this the same night GS came out), the rom I used for Cristal was a clean ROM from Spanish 1.1, so no patches applied there. That's why this whole thing is weird, It shouldn't have triggered even if I wanted to.Well that depends on where you got the .cia.... You couldn't have gotten it from the CDN (even if you did it wouldn't work without the seed; which you can't get until official release) so you have to be using a VC inject of sorts. Even the one I have is the "Official Crystal" injected over Pokemon Gold but the title ID changed to match the place holder on the CDN. So I'm going to assume the one you got was pre-patched, if you didn't do anything but install it.
And yes, I'm aware Pkhex doesn't change any value besides putting the ball on the Key items slot...