When you removed the shaft the first time, its possible that the gear oil seeped past the seal and was just sitting in the axle tube, slowly making its way out. Fairly common when replacing a shaft, especially if the axle was tilted at all when the shaft was removed or if the oil level was above the bottom of the seal. Top off the diff and just keep an eye on it to see if it leaks any more. Also, the total length of the axle shaft being 1/32" different would have no bearing on the seals. What you would want to measure would be the seal surface (diameter and location) which is on the outside of the center section.
2000 WJ 4.5L - Stroked, Locked, & Long-Armed
Looking for 6" WJ springs!