Let's pick this apart a little bit...
1. We've established that both E dials are working, Correct? The way I had mine set on the K7 and have them set on the K5 is as follows...
(on K7, they've moved the e-dial settings to the record menu on the K5)
Custom menu #C4 24 Tv mode is set to 5 (shutter speed rear, ISO Front)
Custom menu #C4 25 Av mode is set to 4 (Aperture Rear, ISO Front)
Custom menu #C4 26 TAv and M mode set to 2 (Shutter Speed Rear, Aperture Front, ISO button used for changing ISO).
I have Auto ISO turned off in every mode that will let me turn it off (hold down the ISO button and turn the rear dial to the left, Hold the ISO button and press the Green button to turn it back on). Digital preview is turned off and optical preview is turned on (Record Menu 3).
I also don't use the green button but use the meter and adjust aperture and shutter accordingly. If you have the electronic level turned on you will not see the meter but rather a Number that represents the exposure (0 is a centered meter).
2. Your Sigma APO is set on A and you've confirmed it's working, Correct? That is, you can go to Av mode and set the aperture to something other than f22 and the lens responds properly. If you go to Tv mode, you can set the shutter speed and the aperture will follow for correct exposure?
3. Forget about the Green button (for now). Look through your viewfinder and tap the shutter release to activate the meter (Lens set on A). At this point you should be able to adjust both the shutter speed and aperture while watching the meter (I use Spot metering BTW). Be careful not to hit the AE-L during this procedure either (I hate where they put that button). You may want to increase the Meter Active time, Custom menu 1 #4, pg 114.
If as set in #3 you half press the shutter release while turning a dial, the camera will behave as if it is in TAv mode with a fixed ISO. That is, it will hold the exposure and depending on which dial you turn, the other should adjust accordingly.
4. Take your lens off of the A setting and choose some value. Now while looking through the viewfinder, pull the preview. This will stop down the lens to your desired aperture (the Aperture will read F-- on the camera and will record as 0). While holding the preview lever, adjust your meter by turning the rear dial changing the shutter speed, assuming you set your camera as I recommended. You can also leave the shutter speed and aperture where they are and adjust the ISO to set your exposure. This is how I set exposure when using M, K, and M42 lenses (the M42 lenses are already stopped down without activating the preview but it still must be done to activate the meter).
To me, M mode is to have Total control over the exposure. The Green button still defeats that purpose. That may just be me though.
So, At what point is your camera failing, or is it operator error? Have you tried a different lens? Does It work? If so and yes, then the problem may be your Siggy APO.