D'oh! Because the camera was set to matrix metering, the flash changed itself automatically from TTL to TTL-BL (backlight). I bet that was the real culprit. Off to do some more tests.
That was my complaint in my first here, there should be a menu to set flash metering mode in the camera (where the metering is done). Spot Metering is inappropriate for balanced flash, but it seems a terrible way to have to set pure TTL mode. A few older flashes had a switch on them to select TTL vs TTL BL directly, but those models are disappearing.
FWIW, the TTL BL is about BaLanced flash, not about the word Back Light. Search the D800 PDF manual for wod Backlight, and it is only found in regard to the illumination of the LCD displays. Hunt for word Balanced, and you find it several places about the flash, like page 185 :
i-TTL balanced fill-flash for digital SLR: Flash emits series of nearly invisible
preflashes (monitor preflashes) immediately before main flash.
Preflashes reflected from objects in all areas of frame are picked up by
RGB sensor with approximately 91K (91,000) pixels and are analyzed in
combination with range information from matrix metering system
to
adjust flash output for natural balance between main subject and
ambient background lighting.
The next paragraph says:
Standard i-TTL flash for digital SLR: Flash output adjusted to bring lighting
in frame to standard level;
brightness of background is not taken into
account. Recommended for shots in which main subject is
emphasized at expense of background details, or when exposure
compensation is used. Standard i-TTL flash for digital SLR is activated
automatically when spot metering is selected.
That is of course TTL BL vs standard TTL. Nikon manuals tend to use the word Subject about the flash lighting, and the word background about the ambient, which is valid of course, and is the result of how things work, but the actual idea here is about balancing flash with ambient. Ambient has to be correct on the background, but ambient plus flash must be correct on the subject. Which means reduced fill flash.
The way things work is that any two lights added will be brighter than the brightest. The idea is that ambient metering meters ambient settings to give a 100% exposure result from ambient. TTL metering also meters flash to give a 100% exposure from flash. But two 100% exposures adds to 200% exposure of the subject, which result is one stop overexposed (if using TTL mode, we have to know to back off with manual negative flash compensation). There's a calculator for this at
https://www.scantips.com/lights/flashbasics4a.html#percent . But what TTL BL mode does is to automatically reduce the flash level to only fill level (typically about -2 EV if in bright sun), to prevent most of the overexposure of two proper exposures added. 100% ambient with the TTL at -2 EV compensation results in only 1/3 EV overexposure of the subject, called Balanced flash. We could also add -1/3 EV Exposure compensation then (which reduces background too), however flash compensation is a bit erratic in TTL BL mode (because the automation continues to also do its thing).
My notion is that TTL vs TTL BL is not a factor about Auto ISO and the 2 EV limit. I was testing with a SB-800 which has the huge luxury of having a TTL vs TTL BL switch on the flash. The fact that flash compensation increases the 2 EV increase allowed was true of pure TTL mode.
However, very sorry, I just got very confused about it, because nothing I can do now will let my D800 advance ISO more than 2 EV above Minimum ISO (with flash). Now (from ISO 400), it holds at ISO 1600 regardless. Flash compensation no longer has any effect on it, yet it clearly did just a bit earlier. I cannot account for any change. It is not metering mode, nor TTL vs TTL BL mode, etc. But now I cannot repeat the previous test, and I have no clue why it changed on me. I still have the captured images that shows it was doing the ISO 2200 and 2500 before, but I cannot repeat it now?