I bet I have your answer --
With the RE 3.5" springs it's common for them to unseat themselves when you flex out. At full flex with the swaybar disco'd your spring will be basically be hanging there, with the only thing holding in place being the bump stops. You could literally move the spring up and down 2 inches.
Because of this, when your supsension comes back down to level height chances are that the spring will not be sitting correctly in the little notch on your axle. Take a look, if it looks like your spring is sitting on the second coil you should flex out with the swaybar disco'd, rotate the spring until the pigtail is sitting in that little notch, and you should be good.
If you find that indeed your spring isn't sitting properly because of the reason above, then you can get a spring retainer clip at the dealership for $12 (for a set of 2 clips and the bolts to hold them). These clips came stock on some '97/'98 TJ's.
Let me know if you need it and I'll post the part #'s.