The way Minecraft is launched changed significantly with 1.6.x. Which is the reason FTB hasn't released anything with 1.6.x yet... the current FTB launcher doesn't work with that Minecraft version. The same reason may be responsible, in the other way around, for locking 1.5.x instances to the vanilla Minecraft directory. Maybe that version simply lacks something the vanilla launcher needs that was only introduced in 1.6.x.