Ore is being generated incorrectly with Thermal Foundation.
I believe the cause of the problem is as follows.
ThermalExpansionPlugin.java
is looking for the file that describes thermal foundation ores with
File configFile = new File(configDir, "/cofh/world/ThermalExpansion-Ores.json");
This file is now /cofh/world/ThermalFoundation-Ores.json