@Deathshades
I just noticed that the having the rate for Resource Train Wagons will cause an overflow. Amounts in Rust cannot be more than 2,147,483,647 and wagons usually start with a number over 2,147, so when multiplied by one million, it can cause errors.
I would suggest making the train modifier no more than 10,000 to be safe.
With that setting lowered, everything worked fine for me. I was able to chop trees, hit nodes, pick plants, use excavators, etc, at a 1,000,000x rate.
Try turning down the Train Wagon number to 10,000 and see if you're still getting any errors.