Hi Yoshi,
Have you started to use a new shower gel or soap at all? Or even a new lubrication or new type of condom, or even a new wash powder??
Whatever new thing you may have used may have chemicals in it that are too harsh for your genital area and this may be an allergic reaction?
If it is an allergic reaction then taking some antihistamine (for a few days) and stopping use of the product that caused the reaction will clear this up.
However, if you have not used anything new and do not think it is an allergic reaction then i would go to the doctor. I dont know of any STI's that cause flaking/reddening on the scrotum as well as the penis..
Also this may be helpful: http://www.nhsdirect.nhs.uk/help/bodykey/Questions/Index.aspx?nodes=odOYuCa7fAU%3d
Go to the above link, answer the questions and see if it leads you to a conclusion.
Good Luck
I'm no expert, but it seems you need to get some type of cream for your doctor