Glad you got a second or was it third opinion that this is how it works...
Unless your using the serial to grey code converter, there is no bits to miss. I suspect that since you have a transponder that does not show the pressure alt that you might be using the converter. (what transponder you using?)
If you are using the converter, the converter could go bad (never heard of this) and start missing bits or you could have a wiring issue or bad connection between the converter and the transponder as a failure mode. If your using this converter, it is not 100% guaranteed since you have another device and way more wires and connections between the EFIS(the encoder) and the transponder.
With straight serial, it either works or it doesn't. There is no in between.
Not sure what other systems you are refering too but I have never seen any Experimental EFIS systems that have a separate display for their encoder output (pressure altitude). Blind encoders don't have em and neither do encoding altimeters?????
In the old days when everyone used grey code and transponders did not display pressure altitude, the only way to know what was up was to have a transponder check done with one of them fancy test sets.
Dynon tech support explained it quite well by indicating that with this system there cannot be any difference between the altitude shown on the display and the altitude transmitted. That is what I needed to know.
With other systems there can be a difference and that is why they have an independent means to show the altitude sent to the transponder. One missing bit and the difference can be hundreds or thousands of feet as I have encountered in the past.
Bill Marvel