Your contract says net profits instead of net sales? How did that get past your agent?
As far as I know it's pretty common with indy publishers now (it is, there are whole threads about it on AW.) Certainly most contracts I've seen recently show that. But I'll go back and check my terminolgy. (The royalty was definitely around 16p per copy, though.)
Just checked - it is a percentage of amount received less publisher's costs.
What the contract doesn't specify - and should, and yes, a miss by the agent, indeed - is a retail sale specification. It only specifies publisher website sales where there is no retailer margin to take into account....
But! And this is a huge but! These net profits contracts have risen since ebooks became significant. Bookstore sales are so mimimal for indy authors, they have very little impact on my royalty - and on this contract my ebook royalties are generous. Since they're by far the bulk of the sales, it more than outweighs the net on paperbacks. But for a bricks and mortar retailer-based model the net-profits model would be significant.