Altimeters are very precise that's why most of the time all three instruments read exactly the same.
So they are allowed to be within a range but it does not mean they are.
Cable velocities are irrelevant as the instrument is calibrated accurately for touchdown.
Difference from the standard ISA temperature will in my opinion be the biggest error in this scenario. Now i could look up the formulas i guess but i'm just gonna be lazy and use an online calc i found, so no guarantees for it to be correct. (
http://newbyte.co.il/calculator.php)
At ISA-10C FL 310 equates to 29967 ft MSL and FL 290 equates to 28031 ft MSL.
Difference is 1936 ft.
So this sounds mostly like what op posted about.
Agg-Karan do you remember the ISA deviation that day?
Now it also measures low because the centers of the airplane are let's say roughly 1960 ft apart for ISA-5 and then you still need to subtract the upper part of the lower aircraft and the lower part (including gear) of the upper aircraft. Which could anywhere from 30 to 70 ft depending on the types etc.
Now on a ISA+15 day the planes would be 2110 ft apart and the radio altimeter would likely read about 2050 ft.
But still ISA deviations definitively plays a big part in what is displayed.