JoelWhite: Then there's a glitch in the system.
Could be. But I assure you the standard functionality is as I described it to you. Only yesterday, I played a match where this happened to my opponent. He exceeded the 90 seconds for one of his shots on hole 3 (I think), so he got a warning and another 90 seconds. Then, he exceeded the 90 seconds on his birdie putt on one of the last few holes, and he immediately received a stroke penalty; there was no second set of 90 seconds. I like this setup.
JoelWhite: Here's a thought, Faterson...would you be acceptable to a 90 second shot clock, with a penalty stroke occurring after said 90 seconds?
Yes, I would. This is how TWO does it. I like WGT's way better, though: first a warning, and if the same thing happens a second time, the penalty stroke is immediately applied. There should be no glitches, of course. And, as I said, I'm very much open to the idea of letting the game host decide what the timer should be: 30/45/60/90 seconds/no timer at all.