Re: Leaky Roof? Post your leaky roof problems here!
Had the same problem after I installed ARB's aftermarket full rack. You have to silicone the bolt holes during the install or you will defininely have leaks. I don't know if this is the same outcome when installing the TRD rack but I suspect it is the same. The supplied grommets are insufficient to seal water out and I used a premium urethane clear seal and have had no leakage problems since.
Pull the bolts and re-install using the premium-grade silicone. I promise your problems will go away.