Bookscan numbers show what is actually being sold at almost all retail stores -- one customer, at the cash register, cha-ching. It doesn't show what the bookstore bought and is sitting around not selling -- it shows what ACTUALLY SOLD. It is absolutely accurate FOR THAT. What it doesn't show, as has been mentioned, are schools, libraries, bookclubs, bookfairs, special sales, bulk sales, many gift shops, and notably among retail stores, WalMart.
One of my publishing friends pulled a big selection of titles across all categories, all types of books, from her publisher and compared the REAL numbers to the bookscan numbers. She found that the bookscan numbers were, as you can imagine, all on the low side. (Obviously, because it is real sales but not all sales, the bookscan number will never show you a too HIGH number). And I've done the same with my own royalty statements.
HOW OFF ARE THEY?
Varies wildly across the board, but depending on the book, anywhere from 10% to 85% INACCURATE.
In other words... don't give yourself a nervous breakdown over it.