This happens in a singleplayer game. I am not running a standalone server. The messages you see in screenshots are those that appear when you change GT6 version between .01 and .02 (images are named accordingly). You should be able to reproduce both of the missing block messages at the very least.
In theory, if this was caused by a new .02 block that appears in worldgen, that block would be reported as being removed when switching to .01 (second screenshot GT6_versionchange_to_6.14.01).
Looking at those block names, the only one I suspect would be part of worldgen is gregtech:gt.block.crystalores
Unless there are magnalium rails in worldgen, of course 
I guess I could mess with worldgen options in a superflat world to see which block causes this? Like, 1 layer bedrock, 1 layer stone and force ores to spawn at the 2 level?