First of all, I am more certain by the day that the screeching IS in fact the undercarriage floating in its locks. This is being looked at and there is some work being done on the hydraulic and other systems. FSX windlayers and turbulance (and OAT) are prone to give "interesting" results (read : crap) . Changes in wind layers will however cause a vertical component due to differences in lift, more or less, attributable to the sudden change in "airspeed", or more correctly, speed through the air mass at THAT particular moment.
Oh, one point courtesy of Dudley, on a question I put very early on in testing...it is a VERY bad idea to touch the brakes to stop wheel spin in these high performance aircraft. The brakes are fairly delicate being designed more to slow the aircraft or manoeuvre it rather than to stop it. Accordingly the use of brakes to stop the wheels when bringing up the gear can cause the brake pads to fuse. This will, if it happens, result in an almost certainly fatal accident on touchdown. I, like almost every other GA pilot, learned to touch brakes to smooth the transition for passengers (even on aircraft with non-retractable gear) and stop some of the strange noises etc that can unnerve inexperienced fliers but it should not be used in these aircraft. As an aside, I never do it anymore in any aircraft, since Dudley's cautionary tale.
The Spitfire does not generally need braking on landing if you use correct technique. It is however vital to peg approach speeds, touchdown angle and heading and to make sure that the throttle closes completely before touchdown. Even an excess of idle rpm (set by the ground crew) needs to be tested for at preflight, as ANY higher than normal idle will cause the Spit to float for miles. Using brakes to cover bad technique is sloppy, lazy and dangerous. The Spitfire I and II had very marginal braking at best.
The fuel slow running cut out effectively "chokes" the engine, making for a more orderly shut down than merely leaving the thing to run out of fuel. The reason that the engine will not "catch" again if the fuel valves are closed is that the SRC-O has dropped the fuel pressure too low for the engine to repressurise the system, given that no MORE fuel can be drawn into the lines. If the fuel taps are open, the system can draw fuel from the tanks to recharge the lines. The behaviour is correct.
There are some inconsistencies and compromises that had to be made. In reality though, every attempt is made to keep some pressure in the system as a Spitfire is perfectly capable of jumping chocks even at quite moderate rpm. Thus ground crew are assumed to recharge the system whenever possible. If there is no pressure, the engine will provide it on startup. That being said, there is no reason for anyone to sit operating flaps repeatedly, or brakes and the only time the lack of pressure would actually affect you is once you are moving...at which point the engine has charged the system anyway. Where compromises need to be made, they are, where possible, made in areas outside normal operations. So if there is a choice between making it work properly whilst flying OR making it work properly when repeated needlessly on a Tuesday by a one legged dwarf who has two maiden aunts named Clarice, the choice is pretty easy.
Best practice is to treat the Spit as a real aircraft.....my routine is this:
1. Load Flight
2. Shift 3 to set cold start (unless saved that way, more usual)
3. Shift 7 to check condition and compression
4. Shift 4 to replenish stores
5. Shift 3 to set chocks, hold tail etc
6. Enter cockpit and begin prestart.
Doing this avoids anomalies, maintains maximum reality and ensures a safe baseline for ops. Nothing different to what I would do in the real world (subject to the computer specific tasks).