I cannot emphasize enough, the value of this thread!!!
I'd be willing to bet that most of the complaints about this flash unit under-exposing in PTTL, can be solved by following the directions in this thread.
I own two 540's, but I rarely use them both. Well I decided to test them and adjust as necessary, based on this thread. I was surprised to find that the one unit was about a full stop under-exposed compared to the other one, and even at that, the better of the two still under-exposed.
On the one flash, I had to adjust the little screw about 1.5 turns CCW, on the other one only about half a turn. Like was mentioned earlier, if you turn it too far you'll drop back to underexposure. At one point all it took was about 1/16 turn and the peak on my histogram dropped all the way to the far left quarter of the graph, and the resulting image was almost too dark to make out. (I shot my living room curtains instead of the carpet.
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Now I have each flash's P-TTL adjusted equally and optimally. The histogram peak is just past halfway on the graph, into the third quarter. That appears to be as good as it gets. I have yet to try either flash out in any other situations, but I'm hoping that the "AF-540 under-exposure problem" is a thing of the past. BUT, you'd think that for such an expensive flash, that they might do this adjustment at the factory before they ship them out, rather than leave it for an ingenious Pentax owner to discover! Again, thanks to the OP for this EXCELLENT information!