I just called Miltek and spoke to someone there due to the annoying ticking we both get and he says they have had reports of this from other people, even Australia!. They suggest its cause by the Valve position, the reason you still have it with your new Miltek is they use Audis valves!. Im sure i saw someone post this too but they just confirmed this.
He suggets this is whats causing the ticking. Since they dont do a none valved version for the RS3 we wont know until someone either has another backbox fitted such as ArmyTrix or has one made.
Miltek did say they have another valve in development but its not ready. I hope it is this cause it was what i was originally told when i had mine taken apart.