Can you repeat that effect? Sorry, I draw a complete blank, I have no clue what it was. Assuming camera did not move aim, and subject didn't move, and nothing changed between the two tries. And nothing blocked the flash, etc. etc. I think it should not happen. We could ponder things like an unknown compensation or something, but such should affect both exposures. FV Lock can be a bit different exposure than without, but mostly it usually seems better. Mine is normally very slightly brighter with FV Lock.
FWIW, a few useful things not well known about FV Lock. It can vary from without FV Lock.
1. It suppresses any D lens distance check from overriding the flash metering, which can help TTL BL direct flash. But TTL mode and/or bounce are not affected by D lens anyway.
2. FV Lock suppresses TTL BL mode balancing. Exif still calls it TTL BL, but the results not distinguishable from TTL (so in that respect, it should serve the same purpose as Spot metering indoors, except would have no ill effect after we go back outside forgetting to reset it). But so does Spot metering, and I cannot believe both Spot and FV Lock on would have any different effect. At least, I cannot duplicate your problem here, with a D800 and SB-800 TTL BL with Spot and FV Lock.
I sure wish Nikon would provide a simple camera menu to select TTL or TTL BL flash metering. Would be so simple to use and explain then.
3. Triggering the FV Lock button will also show the EV warning about insufficient power like the normal flash shows, but early, at FV Lock time. Of course it has to be insufficient to see it, but bounce at f/11 ISO 100 should see it.
1 and 2 must have to be true, since FV is at a different time, and might even be aimed a different direction for the final flash. It can't assume all is still the same.