I had similar issues going from XBR3 to FreeBoot.
The issue, ultimately was (because I had used NandPro) to build XBR.bin image, I hadn't used the CPU key to decrypt the KV.
It turns out that you can flash a xbr.bin to Nand and the console will boot just fine. I did have some stability issues, but overlooked most of them.
The problem was when I was trying to upgrade. Since I was trying to use a Nand Dump (the XBR.bin) that didn't have the correct KeyVault the CPU key I was trying to decrypt with wouldn't work. All tools (FlashTool and Easy Freeboot v2) gave me error or wouldn't output a good bin.
After a few iterations of still getting errors, after using the original (virgin) nand dump with (what I thought was) a good CPU key, I realized I had mis-read a single digit on the CPU key.
Once I had that corrected, (ie I had the RIGHT CPU key) I used Flash Tool with the FreeBoot image (on the original Nand dump) to build a good update bin.
Flashed the new updated bin with Flash360 and after one RROD boot, I waited for 2 minutes, rebooted and everything worked.
So bottom line:
1) Ensure you have a accurate CPU Key. (an accurate key will decrypt the KeyVault from the original dump of the nand in Flashtool)
2) If you need to, use the original NAND to build your new FreeBoot image.
3) reflash nand using your preferred method.
(One issue not discussed here is the SMC update (from the original Nand to the one used best for Freeboot) but that's a topic that is discussed better elsewhere.)
Hope this helps.
S_L