The problem seems to occur when BL3.9FB users attempt a restore/upgrade to 1.0.0, or 1.1.1. Essentially, iTunes thinks that you have no bootloader and then loads a 3.8BL onto your iPhone.
This is a stock 3.8 bootloader so you will not be able to leave BL3.8 unless you open up the phone and testpoint. MuscleNerd has pointed out that all is not lost, because the 3.9 expoits are sill present. However, I would still advise people not to downgrade to 1.0.0 or 1.1.1!
This warning was posted by drg on hackint0sh.