It is getting even more weird . Actually SR "recognizes" your device to be bad and sets the following voltages: 500:34,550:42,600:48 according to your measurements. Those voltages are way above the voltages in your custom OC profile with SR disabled: 500:34,360 550:38,400 600:42
You said you are not able to enable fmtx. Why is that?
Did you ever try a full reflash (both rootfs and eMMC) to see if it makes any difference?
Are you sure there is no some background running script (ala batterypatch) which sets frequency/voltages?