Travel from Pakistan to China, can apply visa from malaysia?

I am Malaysian, currently staying in Pakistan (married to Pakistani). I tried to apply tourist L type entry permit through PRC Embassy in Pakistan but they refused to accomodate me as I am not Pakistani citizen. I will be back soon to Malaysia for the application. My hotel booking/flights has already been prepared by travel agent in Pakistan (will travel from Pakistan to PRC). Will this affect my application in malaysia?