Oh that was a Forge Bug, dont worry about it, I found a workaround and newer GT6 Versions should never have that specific thing happen again. 
Forge is needlessly resetting the Block and Item IDs (to what they were before loading the save file) after the Server shuts down. Guess what happens during Server Shutdown. Right I was saving the Garbage into a File, and Forge decided to randomize all Item and Block IDs.
This reset is absolutely not needed as it sets the Block and Item IDs when loading the Save File too! Its essentially resetting it twice for no reason.