Dan,
I'll second Andy on his appreciation for coming on and giving your perspective. As I said in a previous comment, it's much better to learn from a situation like this than to to sit and argue about whose fault it was. This is good stuff. And you can believe that I will be paying a "little" more attention to that flag station in the future!!
+5!
In regards to the topic at hand:
I strongly believe in a standing yellow before a waving yellow! So what if you lose a passing zone! A standing yellow tells you to ease up a bit and check your surroundings... Whether its a car off the track or a waving yellow at the next station, you know to look for it. This also very simple and easy to implement.
Very reasonable scanners exist that can be tuned to the flagger network. I'd already planned to buy one, but it just got moved up my want list!
We as drivers also need to remember to keep our eyes up, be aware, drive our own line, etc. Part of this is paying attn on the pace lap and looking at all the waving flags. They are not just saying hi, nor are they bored, they are showing us where they are! We HAVE to make a habit of glancing at the station every time we drive by! I follow a basic routine which of course varies, but here is an example: "Track out, check the flag station, check your mirrors, check your gauges, take a deep breath, relax your hands(one at a time), check your mirrors, check the (next) flag station, brake, downshift, turn in..." And if you have to talk to yourself, do it!