I am setting up the Ace I of my niece. I came from the latest Italian stock ROM, after messing up with CM11 Aug 30 (which gets stuck at boot). So I re-flashed the stock ROM with ODIN, installed Raf kernel (w/o modules) and I lost the IMEI: Installed the modules still no IMEI. Now I just installed the Thunderbolt "stock" kernel and the IMEI reappeared.
It must be noticed that Galaxy Tool with Raf kernel did show the IMEI in both the UI "show device" option and in the EFS file (and so there was no way to edit it). It was just the kernel unable to read it.