The biggest issue is the thief is actually correct. The ToS encourages this and will defend them if they do so. It also practically prohibits giving new members access to helpful items the FC chest, technically you can do it but absolutely shouldn't and can be punished for it. In fact you can be punished for giving any member access to the company chest (an officer can clear you out and leave after an argument) or even joining a FC (the leader can lock access to FC rooms and hint that a 2m donation will give permission rank). The ToS allows all of this.
Being rigid to this degree on ToS creates an exploitable game environment. The GM's should be free to act with rational common sense in situations like this.
Another thing that would help too is if you could set a max number of chest withdrawls per day for each rank. For example, you can set that new members can withdraw 5 stacks a day. This cuts losses drastically in the case of theft.
