There is no difference. While you see "as per" used quite often, the "as" is not really needed, but it does add a slight emphasis. It is not wrong, just not really necessary. I guess technically, "per your instructions" means "according to your instructions" and "as per your instructions" means "in accordance with your instructions". There is no real difference in these two terms.

Although "as per" and "according to" mean the same thing, "as per" is mostly used in busines or legal writing and almost never used in speaking. "According to" is used in less formal writing and when speaking. For example： As per our legal counsel, Thunder and White, we have decided to pay you the sum of $1000 because of the faulty plumbing supplies that your received in 2008. Please confirm your acceptance of this offer by return mail. According to the best scientific minds there are likely millions of planets in our galaxy alone where life as we know it is present. The speed of light limit, however, makes it unlikely we will encounter any of that life in our lifetimes. It is the best I can do without getting out of my comfortable chair and finiding a dictionary.