I agree with the above comments regarding programming, lack of desire on the part of the airmen, and not enough time to develop them and see results. Here are some bullets:
1. Pullups are an absolute must and perhaps you just forgot to list them.
2. Isometrics? Don't see that in any posted WODs, but they're ok for warmup.
3. Your scaling is probably hurting some. You determine what gets scaled, not the participant. Tell them what they will lift and what they will do. They'll complain, but that's what you're there for.
4. Your programming seems off. I suggest staying away from making up your WODs on the fly unless you have a lot of experience putting things together. Also, floorwipers are ok for warmups, but not so much for WODs. Also, broncos, flutterkicks, low-crawls? WTF? 100 burpees/1 mile run? Where's the intensity? They'll burn out on the burpees after about 30, schlep through to the end, and then take it easy on the mile. Better might be 5 rounds of 20 burpees/400m run. Keeps the intensity higher. Note that I'm not saying the WOD isn't hard, it's just that the intensity has to drop off because they'll have to slow down just to complete the WOD. The other WOD you list is, again, lacking in intensity for the movements chosen and too focused on the legs without some kind of break. Instead of 5 rds of 10 burpees, 10 thrusters, 30m lunges, try as many rounds as possible in 20 mins of 5 burpees, 10 situps, 15 PVC overhead squats, or 3 rounds of 400m run with (3 rds of 5 pullups, 10 pushups, 15 squats). Try mixing up your time priority and task priority WODs to keep them interested and the intensity up. A chipper every once-in-a-while is okay, but keep things simple if you can (couplets, triplets).
5. Given that most of these folks are probably deconditioned, I would definitely have short, but intense runs at each session coupled with a WOD. This will help them on the run, but will rapidly improve their cardiovascular endurance and stamina.
6. Turn portions of the PT test into buy-ins and cash outs (before and after the WODs). For example, after the warm up, do as many pushups in 2 mins, or as many situps in 2 mins. Make these buy-ins/cash-outs longer in duration, so that the test seems easy. Also, run the entire PT test as one event for a WOD: 800m Run, 50 pushups, 800m run, 50 situps, 800m run OR 3 rounds of 800m run, 50 pushups, 50 situps. This is great for confidence building.
It sounds like command influence on the requirements of your programming appear to negate the CrossFit programming you are trying to do. Also, given that you've only got 5 to 7 sessions, you won't get far without additional training time. Focus on the basics, nine basic movements, bodyweight exercises (and running/sprints are monostructural, not bodyweight), and running 400s and 800s for time. If you can find time to get them into the gym and do some power lifting or Oly lifts, it would help.
In order to really see gains, you'll have to offer up additional training sessions that are truly CrossFit specific (i.e. main site WODs and the like). Does your schedule, and theirs, allow for optional training times during lunch or in the evenings after work? If you're training them now on M/W in the a.m., then perhaps you could offer CrossFit classes on Tu/Th at either noon or 1700. The ones who really care enough to improve their PT scores will show up and train. The ones that don't care, don't care. And you're basically wasting time on them. If you could get them to train 4x/week instead of just 2x, you would see a huge difference. Once you get a few onboard, they'll never go back to the way they trained (or didn't train) before.
If this is truly a leadership course, and improved PT scores are a metric, then more emphasis must be placed on PT training. 2x/week isn't going to cut it. Period. What happened to M-F 6 a.m. PT?
The other recommendation I have is to get in touch with the SEAL instructors at BUDS (or email Dave Castro or Andy Stumpf) to find out what works and what doesn't for their trainees. Granted, they have a more intense PT program than most
, but at least you can get their perspective with regard to what you're doing.
I think that, given sufficient training time with CF, you'll see PT scores improve drastically. Good luck!