M.B.
I would suggest having a your pediatrician evaluate him regarding appearance, use and future complications. I would not think he would have problems later, though anything is possible. Not all genitals look a like. I can attest to even girls having varying shape, color and skinfolds. Even "tags" so to speak. So different is not necessarily cause for concern. Now undiscernable or extreme variation would be. Not appearing flacid may have to do with amount of scar tissue at the site. It is possible more scar tissue to form due to either a genectic condition with you child that causes more than needed scar tissue or poor procedure where more scarring happened due to error. As for "playing" with himself. This is normal, do not make him ashamed. Just remind him that is private to be done in privacy and requires handwashing, just as going potty or getting his boogers.
Here is a link to the best laymen's explanation of freud's psychosexual development http://en.wikipedia.org/wiki/Psychosexual_development
Many prayers that this be nothing and that your son will not be affected.
-MB