I think several factors are interfering with your calculations.
The IG/IGU DME ranges aren't the same as the distance to the threshold because the DME antenna aren't at the threshold. The two different DME's antenna aren't even in the same place. Think of the way to read it as 'When the DME I'm using reads x I will be 3.1nm from the LOC only MAP/3.7nm from the threshold'.
DME distances are rounded to the nearest .1 nm so a slight error may occur. Compare the IG vs IGU ranges vs distance between the IG 4.0 stepdown and the LMM.
DME is a slant range, not an along track distance. The geometry changes as you get closer so that can also affect DME readings vs actual distance.
Speaking of geometry changes, if the DME antenna is located elsewhere on the field than lateral geometry changes will also affect DME reading vs actual distance.
Also the glideslope is typically to the aiming point on the runway ie 300m/1000' further along the runway from the threshold so glideslope calculations will be slightly out if you use the threshold distance.